NAMD-L: By Date

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NAMD-L: By Date

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Starting: Sat Jan 02 2016 - 22:55:30 CST
Ending: Sat Dec 30 2017 - 12:48:03 CST

question about point substitution Aâ†’U parinaz bashirbanaem (Sat Dec 30 2017 - 12:47:43 CST)
Re: Haohao Fu (Fri Dec 29 2017 - 21:36:33 CST)
(no subject) Suresh Ghimire (Fri Dec 29 2017 - 19:57:56 CST)
Re: Having problem with restarting colvar distance, Aliasghar Alizadeh-Mojarad (Fri Dec 29 2017 - 14:46:29 CST)
Having problem with restarting colvar distance, Aliasghar Alizadeh-Mojarad (Fri Dec 29 2017 - 02:10:07 CST)
Re: [NAMD] Question about patches JC Gumbart (Tue Dec 26 2017 - 09:26:12 CST)
RE: [NAMD] Question about patches Lennart Nilsson (Tue Dec 26 2017 - 04:43:30 CST)
Re: [NAMD] Question about patches The Cromicus Productions (Mon Dec 25 2017 - 18:04:43 CST)
Re: [NAMD] Question about patches The Cromicus Productions (Mon Dec 25 2017 - 17:53:36 CST)
Re: [NAMD] Question about patches The Cromicus Productions (Mon Dec 25 2017 - 17:29:06 CST)
RE: [NAMD] Question about patches Lennart Nilsson (Mon Dec 25 2017 - 09:17:51 CST)
Gradual cooling of the system Natalia Ostrowska (Mon Dec 25 2017 - 02:23:11 CST)
Re: [NAMD] Question about patches Natalia Ostrowska (Mon Dec 25 2017 - 01:58:35 CST)
Gradual cooling of the system Monika Madhavi (Sun Dec 24 2017 - 22:27:27 CST)
Re: [NAMD] Question about patches JC Gumbart (Sun Dec 24 2017 - 15:16:10 CST)
[NAMD] Question about patches The Cromicus Productions (Sun Dec 24 2017 - 03:49:07 CST)
(no subject) Suresh Ghimire (Fri Dec 22 2017 - 09:54:23 CST)
Re: facing problem while downloading NAMD Roshan Shrestha (Fri Dec 22 2017 - 03:40:20 CST)
Fwd: facing problem while downloading NAMD Jyoti Sharma (Fri Dec 22 2017 - 03:24:19 CST)
facing problem while downloading NAMD Jyoti Sharma (Fri Dec 22 2017 - 03:20:26 CST)
Re: gbsa Stefano Guglielmo (Wed Dec 20 2017 - 15:57:21 CST)
Re: gbsa Brian Radak (Wed Dec 20 2017 - 11:57:24 CST)
Re: reconstructing pmf Stefano Guglielmo (Wed Dec 20 2017 - 01:55:15 CST)
gbsa Stefano Guglielmo (Tue Dec 19 2017 - 19:55:21 CST)
Re: reconstructing pmf Giacomo Fiorin (Tue Dec 19 2017 - 18:24:46 CST)
Re: reconstructing pmf Stefano Guglielmo (Tue Dec 19 2017 - 18:17:35 CST)
Re: reconstructing pmf Jeff Comer (Tue Dec 19 2017 - 12:52:21 CST)
Re: reconstructing pmf Giacomo Fiorin (Tue Dec 19 2017 - 10:27:09 CST)
Re: reconstructing pmf Jeff Comer (Tue Dec 19 2017 - 09:20:57 CST)
Re: reconstructing pmf Giacomo Fiorin (Tue Dec 19 2017 - 08:08:03 CST)
Re: reconstructing pmf Stefano Guglielmo (Tue Dec 19 2017 - 02:48:53 CST)
Re: reconstructing pmf Giacomo Fiorin (Mon Dec 18 2017 - 19:40:03 CST)
Re: reconstructing pmf Vermaas, Joshua (Mon Dec 18 2017 - 18:35:31 CST)
reconstructing pmf Stefano Guglielmo (Mon Dec 18 2017 - 18:24:15 CST)
Re: tcl used for binary compilation Giacomo Fiorin (Mon Dec 18 2017 - 14:32:23 CST)
tcl used for binary compilation Francesco Pietra (Mon Dec 18 2017 - 14:26:30 CST)
Re: colvars: Error: keyword "translatereference" is not supported, or not recognized in this context. Haohao Fu (Sun Dec 17 2017 - 23:54:10 CST)
colvars: Error: keyword "translatereference" is not supported, or not recognized in this context. Victor Kwan (Sun Dec 17 2017 - 22:35:33 CST)
Re: Unable to run CUDA NAMD but able to run non-CUDA version on Windows Chun Heung Wong (Sat Dec 16 2017 - 07:22:29 CST)
Unable to run CUDA NAMD but able to run non-CUDA version on Windows Chun Heung Wong (Sat Dec 16 2017 - 06:50:06 CST)
FATAL ERROR: Bad global improper count! Nehad Elsalamouny (Fri Dec 15 2017 - 23:53:33 CST)
Re: Script for Terachem QMMM Marcelo C. R. Melo (Thu Dec 14 2017 - 15:45:59 CST)
Re: Define a colvar from other colvars Giacomo Fiorin (Thu Dec 14 2017 - 14:57:56 CST)
Re: Define a colvar from other colvars Bogdan Marekha (Thu Dec 14 2017 - 14:53:11 CST)
Re: Define a colvar from other colvars Vermaas, Joshua (Thu Dec 14 2017 - 14:40:22 CST)
Define a colvar from other colvars Ben Adams (Thu Dec 14 2017 - 13:50:29 CST)
Re: Script for Terachem QMMM Haohao Fu (Thu Dec 14 2017 - 07:13:47 CST)
Script for Terachem QMMM Chris Butch (Thu Dec 14 2017 - 03:29:17 CST)
Re: Periodic molecules in NAMD Haohao Fu (Wed Dec 13 2017 - 22:14:16 CST)
Re: Periodic molecules in NAMD Vermaas, Joshua (Wed Dec 13 2017 - 12:18:31 CST)
Periodic molecules in NAMD Bogdan MAREKHA (Wed Dec 13 2017 - 05:13:54 CST)
Re: atom selection error Shahee Islam (Tue Dec 12 2017 - 01:31:22 CST)
Re: atom selection error Peter Freddolino (Mon Dec 11 2017 - 14:26:26 CST)
Re: atom selection error Vermaas, Joshua (Mon Dec 11 2017 - 11:28:09 CST)
Re: atom selection error Brian Radak (Mon Dec 11 2017 - 11:14:36 CST)
Re: atom selection error Atanu Maity (Mon Dec 11 2017 - 08:30:55 CST)
Re: atom selection error Shahee Islam (Mon Dec 11 2017 - 00:52:18 CST)
Re: atom selection error Peter Freddolino (Mon Dec 11 2017 - 00:38:19 CST)
Re: atom selection error Shahee Islam (Mon Dec 11 2017 - 00:33:38 CST)
Re: atom selection error Peter Freddolino (Mon Dec 11 2017 - 00:24:47 CST)
Re: atom selection error Shahee Islam (Mon Dec 11 2017 - 00:04:47 CST)
RE: Free energy did not converge by using ABF Nielsen, Steven (Fri Dec 08 2017 - 15:01:55 CST)
RE: Free energy did not converge by using ABF Jeffrey Potoff (Fri Dec 08 2017 - 13:22:44 CST)
Re: Re: metadynamics run in NAMD or using plumed in NAMD Rabeta Yeasmin (Fri Dec 08 2017 - 12:39:49 CST)
Re: Re: metadynamics run in NAMD or using plumed in NAMD Giacomo Fiorin (Fri Dec 08 2017 - 12:19:43 CST)
Re: Re: metadynamics run in NAMD or using plumed in NAMD Rabeta Yeasmin (Fri Dec 08 2017 - 12:14:11 CST)
Re: atom selection error Peter Freddolino (Fri Dec 08 2017 - 11:54:00 CST)
Re: atom selection error Brian Radak (Fri Dec 08 2017 - 10:41:57 CST)
Re: Free energy did not converge by using ABF Giacomo Fiorin (Fri Dec 08 2017 - 09:27:21 CST)
Re: namd-l digest V1 #2316 Yaxin An (Fri Dec 08 2017 - 09:06:19 CST)
Re: Free energy did not converge by using ABF Yaxin An (Fri Dec 08 2017 - 08:57:01 CST)
Re: atom selection error Shahee Islam (Fri Dec 08 2017 - 08:22:51 CST)
Re: atom selection error Peter Freddolino (Fri Dec 08 2017 - 07:59:51 CST)
Re: Re: metadynamics run in NAMD or using plumed in NAMD Giacomo Fiorin (Fri Dec 08 2017 - 07:08:36 CST)
atom selection error Shahee Islam (Fri Dec 08 2017 - 02:33:19 CST)
Re: metadynamics run in NAMD or using plumed in NAMD Rabeta Yeasmin (Fri Dec 08 2017 - 02:06:22 CST)
Re: metadynamics run in NAMD or using plumed in NAMD Rabeta Yeasmin (Fri Dec 08 2017 - 01:53:49 CST)
Re: Free energy did not converge by using ABF Vermaas, Joshua (Thu Dec 07 2017 - 19:23:53 CST)
Re: metadynamics run in NAMD or using plumed in NAMD yjcoshc (Thu Dec 07 2017 - 19:22:06 CST)
metadynamics run in NAMD or using plumed in NAMD Rabeta Yeasmin (Thu Dec 07 2017 - 17:49:22 CST)
Free energy did not converge by using ABF Yaxin An (Thu Dec 07 2017 - 17:22:31 CST)
Re: nvt vs nve file NEHÄ°R NALINCI (Tue Dec 05 2017 - 00:42:47 CST)
Re: nvt vs nve file Roshan Shrestha (Mon Dec 04 2017 - 18:20:49 CST)
Re: Colvar Error Souvik Sinha (Mon Dec 04 2017 - 12:34:36 CST)
Re: nvt vs nve file Vermaas, Joshua (Mon Dec 04 2017 - 12:26:59 CST)
Re: nvt vs nve file Giacomo Fiorin (Mon Dec 04 2017 - 12:21:34 CST)
nvt vs nve file NEHÄ°R NALINCI (Mon Dec 04 2017 - 12:11:27 CST)
Re: Colvar Error Souvik Sinha (Mon Dec 04 2017 - 08:37:09 CST)
Re: Colvar Error Giacomo Fiorin (Mon Dec 04 2017 - 08:03:05 CST)
Colvar Error Souvik Sinha (Mon Dec 04 2017 - 07:33:12 CST)
Re: Shahee Islam (Mon Dec 04 2017 - 03:57:36 CST)
Re: colvars/rmsd: Error: definition for atom group "atoms" not found. Victor Kwan (Sun Dec 03 2017 - 15:15:38 CST)
Re: colvars/rmsd: Error: definition for atom group "atoms" not found. Bogdan Marekha (Sun Dec 03 2017 - 06:35:28 CST)
colvars/rmsd: Error: definition for atom group "atoms" not found. Victor Kwan (Sun Dec 03 2017 - 05:12:06 CST)
Re: Vermaas, Joshua (Fri Dec 01 2017 - 08:35:31 CST)
(no subject) Shahee Islam (Fri Dec 01 2017 - 02:28:17 CST)
Re: [NAMD] Patch 5MC2 The Cromicus Productions (Thu Nov 30 2017 - 12:25:55 CST)
[NAMD] Patch 5MC2 The Cromicus Productions (Wed Nov 29 2017 - 17:45:16 CST)
Re: Electric field simulation: eFieldNormalized Giacomo Fiorin (Wed Nov 29 2017 - 08:48:05 CST)
Targeted MD, "Biased atoms" and "Fitted atoms", RMSD é»„å§å§® (Wed Nov 29 2017 - 07:27:15 CST)
Electric field simulation: eFieldNormalized Carlo Guardiani (Tue Nov 28 2017 - 13:53:57 CST)
Re: nan for Drude's LP in distance-like colvars Giacomo Fiorin (Fri Nov 24 2017 - 12:31:37 CST)
nan for Drude's LP in distance-like colvars Bogdan MAREKHA (Fri Nov 24 2017 - 10:44:01 CST)
Re: REMD using NAMD 2.13 Aliasghar Alizadeh-Mojarad (Wed Nov 22 2017 - 17:14:40 CST)
SMP instructions for multi-node calculation on POWER 8 + P100 Adrien Cerdan (Wed Nov 22 2017 - 10:09:51 CST)
Re: RATTLE error with lipid bilayer system Vermaas, Joshua (Tue Nov 21 2017 - 14:22:05 CST)
RATTLE error with lipid bilayer system Ahmad Kiani Karanji (Tue Nov 21 2017 - 13:08:46 CST)
Re: NAMD energy run in VMD Peter Freddolino (Tue Nov 21 2017 - 13:02:07 CST)
NAMD energy run in VMD Srijita Paul (Tue Nov 21 2017 - 09:43:08 CST)
Improper section for parameterization Theodora Teddy (Tue Nov 21 2017 - 07:20:59 CST)
Re: missing parameters. Lennart Nilsson (Mon Nov 20 2017 - 11:54:32 CST)
Re: missing parameters. Vermaas, Joshua (Mon Nov 20 2017 - 11:08:47 CST)
Re: missing parameters. Brian Radak (Mon Nov 20 2017 - 08:33:41 CST)
Re: REMD using NAMD 2.13 Brian Radak (Mon Nov 20 2017 - 08:29:29 CST)
Re: missing parameters. NEHÄ°R NALINCI (Mon Nov 20 2017 - 05:32:44 CST)
Re: Bias-exchange metadynamics Giacomo Fiorin (Sun Nov 19 2017 - 17:30:49 CST)
Re: REMD using NAMD 2.13 Aliasghar Alizadeh-Mojarad (Sat Nov 18 2017 - 18:03:41 CST)
Re: REMD using NAMD 2.13 Chitrak Gupta (Sat Nov 18 2017 - 17:58:53 CST)
Re: REMD using NAMD 2.13 Vermaas, Joshua (Fri Nov 17 2017 - 18:16:43 CST)
REMD using NAMD 2.13 Aliasghar Alizadeh-Mojarad (Fri Nov 17 2017 - 18:02:46 CST)
Bias-exchange metadynamics Azadeh Alavizargar (Fri Nov 17 2017 - 05:07:56 CST)
Re: missing parameters. Giacomo Fiorin (Thu Nov 16 2017 - 06:19:04 CST)
Re: missing parameters. NEHÄ°R NALINCI (Thu Nov 16 2017 - 01:28:42 CST)
Re: missing parameters. Brian Radak (Wed Nov 15 2017 - 08:10:46 CST)
NPT simulations with PLUMED in NAMD Eric Lang (Wed Nov 15 2017 - 07:58:27 CST)
missing parameters. NEHÄ°R NALINCI (Wed Nov 15 2017 - 06:53:06 CST)
AW: Change pressure during simulation Norman Geist (Wed Nov 15 2017 - 01:28:06 CST)
Change pressure during simulation Monika Madhavi (Wed Nov 15 2017 - 01:07:39 CST)
Re: NAMD QM/MM Marcelo C. R. Melo (Tue Nov 14 2017 - 11:39:49 CST)
NAMD QM/MM Constanza Galaz Araya (Tue Nov 14 2017 - 10:08:45 CST)
Re: Running multiple-replicas metadynamics Giacomo Fiorin (Tue Nov 14 2017 - 09:07:43 CST)
SMD: constant velocity output analysis (Develop force and displacement plot) Keshab Thapa (Mon Nov 13 2017 - 17:20:38 CST)
Using Gromacs topology in NAMD Amali Guruge (Sun Nov 12 2017 - 22:19:43 CST)
Re: About the performance of RAMD Francesco Pietra (Sat Nov 11 2017 - 00:46:49 CST)
Re: About the performance of RAMD vlad.cojocaru_at_mpi-muenster.mpg.de (Fri Nov 10 2017 - 13:38:17 CST)
Re: About the performance of RAMD Giacomo Fiorin (Fri Nov 10 2017 - 13:14:40 CST)
About the performance of RAMD Francesco Pietra (Fri Nov 10 2017 - 10:55:42 CST)
Re: Psf file generation with Gromacs Parameters Amali Guruge (Thu Nov 09 2017 - 19:45:28 CST)
Re: Running multiple-replicas metadynamics Giacomo Fiorin (Thu Nov 09 2017 - 17:45:50 CST)
Re: Error on Settle.C when compiling NAMD with Intel Compiler Giacomo Fiorin (Thu Nov 09 2017 - 16:12:41 CST)
Re: Error on Settle.C when compiling NAMD with Intel Compiler Florian Blanc (Thu Nov 09 2017 - 11:00:09 CST)
Downloads are .tar files but have .tar.gz extension Toon Verstraelen (Thu Nov 09 2017 - 05:07:26 CST)
Re: NAMD job termination Chitrak Gupta (Wed Nov 08 2017 - 21:17:25 CST)
Re: NAMD job termination Richard Overstreet (Wed Nov 08 2017 - 21:08:32 CST)
NAMD job termination Amali Guruge (Wed Nov 08 2017 - 21:01:25 CST)
Re: Psf file generation with Gromacs Parameters Fotis Baltoumas (Wed Nov 08 2017 - 17:43:42 CST)
Re: Psf file generation with Gromacs Parameters Amali Guruge (Wed Nov 08 2017 - 17:17:14 CST)
Re: Running multiple-replicas metadynamics Giacomo Fiorin (Wed Nov 08 2017 - 16:50:17 CST)
Re: Running multiple-replicas metadynamics Giacomo Fiorin (Wed Nov 08 2017 - 15:49:54 CST)
Re: Running multiple-replicas metadynamics Prapasiri Pongprayoon (Wed Nov 08 2017 - 15:37:51 CST)
Re: Running multiple-replicas metadynamics Giacomo Fiorin (Wed Nov 08 2017 - 05:58:38 CST)
Re: RMSD colvar not working in NAMD2.12 Linux version Giacomo Fiorin (Wed Nov 08 2017 - 05:40:19 CST)
RMSD colvar not working in NAMD2.12 Linux version Abhaysinh Gaikwad (Tue Nov 07 2017 - 21:46:28 CST)
Re: problem in writing the coor files Fidan Sumbul (Tue Nov 07 2017 - 02:55:40 CST)
Re: problem in writing the coor files Haohao Fu (Mon Nov 06 2017 - 23:27:01 CST)
Re: Psf file generation with Gromacs Parameters Haohao Fu (Mon Nov 06 2017 - 23:22:05 CST)
Psf file generation with Gromacs Parameters Amali Guruge (Mon Nov 06 2017 - 19:53:58 CST)
Re: Running multiple-replicas metadynamics Prapasiri Pongprayoon (Mon Nov 06 2017 - 16:35:51 CST)
problem in writing the coor files Fidan Sumbul (Mon Nov 06 2017 - 11:11:28 CST)
Re: Running multiple-replicas metadynamics Giacomo Fiorin (Sun Nov 05 2017 - 10:17:13 CST)
Re: Running multiple-replicas metadynamics Vermaas, Joshua (Fri Nov 03 2017 - 19:05:18 CDT)
Re: RMSD of backbone changes rapidly at the beginning of production run Monika Madhavi (Fri Nov 03 2017 - 18:45:34 CDT)
Running multiple-replicas metadynamics Prapasiri Pongprayoon (Fri Nov 03 2017 - 18:30:11 CDT)
Re: Some water molecules are missing in psf Giacomo Fiorin (Fri Nov 03 2017 - 08:49:48 CDT)
Re: RMSD of backbone changes rapidly at the beginning of production run Fidan Sumbul (Fri Nov 03 2017 - 06:27:42 CDT)
Re: RMSD of backbone changes rapidly at the beginning of production run Peter Freddolino (Thu Nov 02 2017 - 20:25:17 CDT)
Re: Some water molecules are missing in psf Vermaas, Joshua (Thu Nov 02 2017 - 18:13:28 CDT)
Re: RMSD of backbone changes rapidly at the beginning of production run Vermaas, Joshua (Thu Nov 02 2017 - 17:59:45 CDT)
Some water molecules are missing in psf Amali Guruge (Thu Nov 02 2017 - 17:33:06 CDT)
Re: RMSD of backbone changes rapidly at the beginning of production run Monika Madhavi (Thu Nov 02 2017 - 17:28:24 CDT)
Re: RMSD of backbone changes rapidly at the beginning of production run Peter Freddolino (Thu Nov 02 2017 - 09:02:13 CDT)
RMSD of backbone changes rapidly at the beginning of production run Monika Madhavi (Thu Nov 02 2017 - 04:52:11 CDT)
Re: Which NAMD-Build for my local HPC? Giacomo Fiorin (Wed Nov 01 2017 - 08:30:27 CDT)
Re: Which NAMD-Build for my local HPC? Bassam Haddad (Tue Oct 31 2017 - 15:50:19 CDT)
Which NAMD-Build for my local HPC? Bassam Haddad (Tue Oct 31 2017 - 13:34:12 CDT)
Re: Fwd: About wall clock time Giacomo Fiorin (Fri Oct 27 2017 - 08:39:25 CDT)
Re: Fwd: About wall clock time Rik Chakraborty (Thu Oct 26 2017 - 23:09:27 CDT)
Re: [NAMD] Too many collective variables? Giacomo Fiorin (Thu Oct 26 2017 - 15:34:51 CDT)
[NAMD] Too many collective variables? The Cromicus Productions (Thu Oct 26 2017 - 15:11:19 CDT)
Re: Error on Settle.C when compiling NAMD with Intel Compiler Giacomo Fiorin (Thu Oct 26 2017 - 13:56:26 CDT)
Re: Error on Settle.C when compiling NAMD with Intel Compiler Florian Blanc (Thu Oct 26 2017 - 12:34:06 CDT)
Re: Stack Traceback problem in colvar restrain PRITI ROY (Thu Oct 26 2017 - 07:35:09 CDT)
Re: Error on Settle.C when compiling NAMD with Intel Compiler Vermaas, Joshua (Wed Oct 25 2017 - 16:01:57 CDT)
Re: Error on Settle.C when compiling NAMD with Intel Compiler Victor Ovchinnikov (Wed Oct 25 2017 - 15:59:42 CDT)
Error on Settle.C when compiling NAMD with Intel Compiler Florian Blanc (Wed Oct 25 2017 - 15:26:57 CDT)
Re: Stack Traceback problem in colvar restrain Giacomo Fiorin (Wed Oct 25 2017 - 12:19:16 CDT)
Re: Stack Traceback problem in colvar restrain PRITI ROY (Wed Oct 25 2017 - 12:11:52 CDT)
Re: Stack Traceback problem in colvar restrain Giacomo Fiorin (Wed Oct 25 2017 - 10:55:59 CDT)
Amber force filed input failure on GPU Bata ZsÃ³fia (Wed Oct 25 2017 - 10:40:06 CDT)
Stack Traceback problem in colvar restrain PRITI ROY (Wed Oct 25 2017 - 07:46:57 CDT)
Re: namd-l digest V1 #2289 Abhishek TYAGI (Wed Oct 25 2017 - 05:42:24 CDT)
Re: namd-l digest V1 #2289 Zahra Mohammadi (Wed Oct 25 2017 - 02:58:36 CDT)
Re: FATAL ERROR: cuda_check_progress polled 1000000 times over ... Abhishek TYAGI (Tue Oct 24 2017 - 06:42:32 CDT)
FATAL ERROR: cuda_check_progress polled 1000000 times over ... Zahra Mohammadi (Tue Oct 24 2017 - 06:12:55 CDT)
Simulation crashes on GPU Mohan maruthi sena (Tue Oct 24 2017 - 05:25:10 CDT)
Restarting FEP calculations Sadegh Faramarzi Ganjabad (Mon Oct 23 2017 - 15:10:55 CDT)
flat and smooth energy? Brian Radak (Mon Oct 23 2017 - 14:07:13 CDT)
Re: Water atoms' explosion out of solvate box in my RBCG simulation on NAMD Florian Blanc (Mon Oct 23 2017 - 06:03:14 CDT)
Water atoms' explosion out of solvate box in my RBCG simulation on NAMD ThatMind TV (Mon Oct 23 2017 - 05:57:39 CDT)
Enhanced sampling methods for oligomers Jacob Usadi (Fri Oct 20 2017 - 15:33:34 CDT)
AW: building system with or without water for metadynamics Norman Geist (Wed Oct 18 2017 - 01:35:32 CDT)
Re: building system with or without water for metadynamics Giacomo Fiorin (Tue Oct 17 2017 - 21:34:55 CDT)
Re: building system with or without water for metadynamics Vermaas, Joshua (Tue Oct 17 2017 - 19:06:12 CDT)
building system with or without water for metadynamics Rabeta Yeasmin (Tue Oct 17 2017 - 16:52:38 CDT)
Re: Fwd: About wall clock time Giacomo Fiorin (Tue Oct 17 2017 - 09:25:13 CDT)
Re: colvars: Did the orthogonality requirements of colvars change in ABF? JÃ©rÃ´me HÃ©nin (Tue Oct 17 2017 - 08:23:44 CDT)
Re: colvars: Did the orthogonality requirements of colvars change in ABF? yjcoshc (Mon Oct 16 2017 - 22:23:06 CDT)
Re: colvars: Did the orthogonality requirements of colvars change in ABF? Giacomo Fiorin (Mon Oct 16 2017 - 21:43:40 CDT)
colvars: Did the orthogonality requirements of colvars change in ABF? yjcoshc (Mon Oct 16 2017 - 20:20:29 CDT)
sortreplicas on Stampede 2 Chitrak Gupta (Mon Oct 16 2017 - 14:34:15 CDT)
Re: Fwd: About wall clock time Giacomo Fiorin (Mon Oct 16 2017 - 12:16:29 CDT)
Re: Running 2.12 Vermaas, Joshua (Mon Oct 16 2017 - 12:07:07 CDT)
Re: Fwd: About wall clock time Chitrak Gupta (Mon Oct 16 2017 - 08:48:38 CDT)
Re: Fwd: About wall clock time Renfro, Michael (Mon Oct 16 2017 - 08:18:27 CDT)
Fwd: About wall clock time Rik Chakraborty (Mon Oct 16 2017 - 01:20:40 CDT)
Running 2.12 Dr. Eddie (Fri Oct 13 2017 - 19:56:46 CDT)
Re: Implementation of sortreplicas executable for restarted REST2 simulations Bhati, Agastya (Thu Oct 12 2017 - 09:00:27 CDT)
Re: Implementation of sortreplicas executable for restarted REST2 simulations Chitrak Gupta (Thu Oct 12 2017 - 08:21:09 CDT)
Re: Implementation of sortreplicas executable for restarted REST2 simulations Bhati, Agastya (Thu Oct 12 2017 - 06:50:40 CDT)
Re: Implementation of sortreplicas executable for restarted REST2 simulations Chitrak Gupta (Wed Oct 11 2017 - 20:20:24 CDT)
Re: Implementation of sortreplicas executable for restarted REST2 simulations Bhati, Agastya (Wed Oct 11 2017 - 14:50:46 CDT)
REST2 simulations: Corecting shifted dcd files! Bhati, Agastya (Wed Oct 11 2017 - 14:36:14 CDT)
Re: Implementation of sortreplicas executable for restarted REST2 simulations Chitrak Gupta (Wed Oct 11 2017 - 14:32:54 CDT)
Re: Optimizing namd run Vermaas, Joshua (Wed Oct 11 2017 - 14:14:01 CDT)
Implementation of sortreplicas executable for restarted REST2 simulations Bhati, Agastya (Wed Oct 11 2017 - 14:12:44 CDT)
Optimizing namd run Dr. Eddie (Wed Oct 11 2017 - 13:04:29 CDT)
Re: FATAL ERROR: Duplicate bond when going from nvt to npt Marlon Sidore (Mon Oct 09 2017 - 04:04:17 CDT)
Movement of chloride ions during MD Luba Simhaev (Sun Oct 08 2017 - 06:21:53 CDT)
Re: Sample umbrella sampling input file Vermaas, Joshua (Fri Oct 06 2017 - 17:35:33 CDT)
Sample umbrella sampling input file Rabeta Yeasmin (Fri Oct 06 2017 - 17:14:02 CDT)
Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation Brian Radak (Fri Oct 06 2017 - 14:28:56 CDT)
Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation Sadegh Faramarzi Ganjabad (Fri Oct 06 2017 - 14:19:56 CDT)
Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation Brian Radak (Fri Oct 06 2017 - 14:11:27 CDT)
Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation Sadegh Faramarzi Ganjabad (Fri Oct 06 2017 - 14:04:39 CDT)
Re: NAMD on Stampede 2 Chitrak Gupta (Fri Oct 06 2017 - 11:04:16 CDT)
Re: NAMD on Stampede 2 Vermaas, Joshua (Fri Oct 06 2017 - 10:43:59 CDT)
Re: NAMD on Stampede 2 Giacomo Fiorin (Fri Oct 06 2017 - 09:08:35 CDT)
Re: NAMD on Stampede 2 Chitrak Gupta (Fri Oct 06 2017 - 08:32:30 CDT)
Re: Constrain on DNA when using ABF for protein-DNA system Vlad Cojocaru (Fri Oct 06 2017 - 08:28:43 CDT)
Re: Constrain on DNA when using ABF for protein-DNA system Giacomo Fiorin (Fri Oct 06 2017 - 08:15:40 CDT)
Re: Constrain on DNA when using ABF for protein-DNA system Vlad Cojocaru (Fri Oct 06 2017 - 08:08:33 CDT)
Re: NAMD on Stampede 2 Giacomo Fiorin (Fri Oct 06 2017 - 07:50:50 CDT)
NAMD on Stampede 2 Chitrak Gupta (Thu Oct 05 2017 - 18:23:05 CDT)
Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation Brian Radak (Thu Oct 05 2017 - 15:30:28 CDT)
Fwd: Klaus Schulten Memorial Symposium, registration and accommodation David Hardy (Thu Oct 05 2017 - 15:29:08 CDT)
convergence criterion of free energy perturbation (FEP) simulations for pKa calculation Sadegh Faramarzi Ganjabad (Thu Oct 05 2017 - 13:36:07 CDT)
Constrain on DNA when using ABF for protein-DNA system Mehdi Bagherpour (Thu Oct 05 2017 - 13:25:33 CDT)
Re: NAMDEnergy with xtc file Brian Radak (Thu Oct 05 2017 - 07:39:03 CDT)
Re: NAMDEnergy with xtc file Fotis Baltoumas (Thu Oct 05 2017 - 05:29:44 CDT)
NAMDEnergy with xtc file Sneha M (Thu Oct 05 2017 - 05:11:37 CDT)
excluding ions based on mass Olya Kravchenko (Wed Oct 04 2017 - 14:38:44 CDT)
Re: ion moving laterally during Umbrella Sampling? Giacomo Fiorin (Wed Oct 04 2017 - 12:05:39 CDT)
Re: ion moving laterally during Umbrella Sampling? Olya Kravchenko (Wed Oct 04 2017 - 11:48:43 CDT)
Re: ion moving laterally during Umbrella Sampling? Giacomo Fiorin (Tue Oct 03 2017 - 15:16:01 CDT)
ion moving laterally during Umbrella Sampling? Olya Kravchenko (Tue Oct 03 2017 - 12:45:09 CDT)
Re: [NAMD] Running NAMD in Stampede2 Chitrak Gupta (Sun Oct 01 2017 - 19:21:52 CDT)
Re: colvars: keepFreeEnergyFiles doesn't work in latest colvars version yjcoshc_at_gmail.com (Sat Sep 30 2017 - 22:41:30 CDT)
Re: colvars: keepFreeEnergyFiles doesn't work in latest colvars version Giacomo Fiorin (Sat Sep 30 2017 - 12:32:26 CDT)
colvars: keepFreeEnergyFiles doesn't work in latest colvars version yjcoshc (Fri Sep 29 2017 - 21:38:13 CDT)
Re: Building namd 2.12 from source an ARM64 architecture istamkos_at_auth.gr (Fri Sep 29 2017 - 17:38:21 CDT)
Re: performance of NAMD on KNL Vermaas, Joshua (Fri Sep 29 2017 - 16:49:40 CDT)
performance of NAMD on KNL jing liang (Fri Sep 29 2017 - 15:10:04 CDT)
[NAMD] Running NAMD in Stampede2 The Cromicus Productions (Fri Sep 29 2017 - 14:59:34 CDT)
Re: Building namd 2.12 from source an ARM64 architecture Fotis Baltoumas (Wed Sep 27 2017 - 18:15:36 CDT)
Re: Building namd 2.12 from source an ARM64 architecture Vermaas, Joshua (Wed Sep 27 2017 - 18:09:31 CDT)
Building namd 2.12 from source an ARM64 architecture istamkos_at_auth.gr (Wed Sep 27 2017 - 17:06:00 CDT)
Re: margin and pressure in CUDA version JC Gumbart (Wed Sep 27 2017 - 12:55:49 CDT)
margin and pressure in CUDA version JC Gumbart (Wed Sep 27 2017 - 11:48:52 CDT)
Re: minimum CUDA compute capability required for NAMD2.12 David Hardy (Sun Sep 24 2017 - 10:31:29 CDT)
minimum CUDA compute capability required for NAMD2.12 Albers, Thomas (Sat Sep 23 2017 - 16:03:24 CDT)
Re: displacement of protein Ajasja LjubetiÄ (Fri Sep 22 2017 - 02:29:00 CDT)
How to sample pressure from NAMD log file. Daipayan Sarkar (Thu Sep 21 2017 - 22:16:54 CDT)
displacement of protein EstefanÃa Hugo (Thu Sep 21 2017 - 09:08:19 CDT)
Re: Build NAMD with CUDA for unix workstation (centos 7) Haohao Fu (Wed Sep 20 2017 - 03:25:16 CDT)
Re: Build NAMD with CUDA for unix workstation (centos 7) Daipayan Sarkar (Wed Sep 20 2017 - 03:04:32 CDT)
Re: Build NAMD with CUDA for unix workstation (centos 7) Haohao Fu (Wed Sep 20 2017 - 02:22:17 CDT)
Build NAMD with CUDA for unix workstation (centos 7) Daipayan Sarkar (Wed Sep 20 2017 - 01:54:25 CDT)
Re: FAD parameter and topology files Peter Freddolino (Tue Sep 19 2017 - 23:41:42 CDT)
FAD parameter and topology files amit kumar (Tue Sep 19 2017 - 23:12:39 CDT)
Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? JÃ©rÃ´me HÃ©nin (Tue Sep 19 2017 - 13:03:04 CDT)
Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? Victoria Lim (Tue Sep 19 2017 - 12:39:34 CDT)
RE: What is the exact form of the harmonic potential used by the NAMD "constraints" option? Lennart Nilsson (Tue Sep 19 2017 - 12:29:33 CDT)
Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? Giacomo Fiorin (Tue Sep 19 2017 - 12:23:46 CDT)
Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? Brian Radak (Tue Sep 19 2017 - 11:39:05 CDT)
Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? Victoria Lim (Tue Sep 19 2017 - 11:33:46 CDT)
Re: What is the exact form of the harmonic potential used by the NAMD "constraints" option? Brian Radak (Tue Sep 19 2017 - 08:30:20 CDT)
What is the exact form of the harmonic potential used by the NAMD "constraints" option? Victoria Lim (Tue Sep 19 2017 - 01:37:21 CDT)
Re: QM/MM With Mopac Error Marcelo C. R. Melo (Fri Sep 15 2017 - 07:36:26 CDT)
performance is more poor for namd 2.12 Yi Huizhan (Wed Sep 13 2017 - 22:25:13 CDT)
QM/MM With Mopac Error Nisler, Collin R. (Wed Sep 13 2017 - 15:27:19 CDT)
Re: Ion type in NAMD Implicit solvent model for ionizing the system Brian Radak (Wed Sep 13 2017 - 09:59:27 CDT)
Re: Ion type in NAMD Implicit solvent model for ionizing the system Chitrak Gupta (Wed Sep 13 2017 - 09:26:11 CDT)
Re: Ion type in NAMD Implicit solvent model for ionizing the system Roshan Shrestha (Wed Sep 13 2017 - 00:49:39 CDT)
Ion type in NAMD Implicit solvent model for ionizing the system Susmita Ghosh (Wed Sep 13 2017 - 00:31:50 CDT)
[NAMD] Simulations in guanidinium chloride The Cromicus Productions (Tue Sep 12 2017 - 15:57:13 CDT)
Re: QM/MM Parallel Computing With Orca Nisler, Collin R. (Tue Sep 12 2017 - 11:08:47 CDT)
Re: pairInteraction and PME? David Hardy (Tue Sep 12 2017 - 11:05:23 CDT)
Re: QM/MM Parallel Computing With Orca Marcelo C. R. Melo (Tue Sep 12 2017 - 09:45:08 CDT)
QM/MM Parallel Computing With Orca Nisler, Collin R. (Tue Sep 12 2017 - 09:12:59 CDT)
[NAMD] File Missing in Nanopore Tutorial The Cromicus Productions (Mon Sep 11 2017 - 22:38:23 CDT)
pairInteraction and PME? Michael LeVine (Mon Sep 11 2017 - 19:20:59 CDT)
Re: Molecule-based Electrostatics Cutoff? David Hardy (Mon Sep 11 2017 - 17:21:11 CDT)
Molecule-based Electrostatics Cutoff? David Huggins (Mon Sep 11 2017 - 16:58:59 CDT)
Re: extracting avarage pdb from dcd file Souvik Sinha (Mon Sep 11 2017 - 10:19:51 CDT)
Re: applying constant force on water molecules in a particular direction JÃ©rÃ´me HÃ©nin (Mon Sep 11 2017 - 05:12:50 CDT)
Re: applying constant force on water molecules in a particular direction Sanjib Paul (Mon Sep 11 2017 - 01:22:48 CDT)
extracting avarage pdb from dcd file Srijita Paul (Mon Sep 11 2017 - 00:48:06 CDT)
Re: minimization error Peter Freddolino (Sat Sep 09 2017 - 22:51:23 CDT)
minimization error Natasha Gupta (Fri Sep 08 2017 - 19:48:14 CDT)
Re: Dihedral colvar Giacomo Fiorin (Fri Sep 08 2017 - 14:54:44 CDT)
Re: Dihedral colvar PRITI ROY (Fri Sep 08 2017 - 14:33:45 CDT)
Re: Dihedral colvar Vermaas, Joshua (Fri Sep 08 2017 - 14:06:25 CDT)
Re: Dihedral colvar PRITI ROY (Fri Sep 08 2017 - 13:55:01 CDT)
Re: Dihedral colvar PRITI ROY (Fri Sep 08 2017 - 08:44:31 CDT)
Re: The number of QM atoms received is different than expected Haohao Fu (Fri Sep 08 2017 - 04:23:59 CDT)
The number of QM atoms received is different than expected Haohao Fu (Fri Sep 08 2017 - 04:01:24 CDT)
Re: Free MD simulation (Production run) Roshan Shrestha (Fri Sep 08 2017 - 02:36:04 CDT)
Free MD simulation (Production run) Roshan Shrestha (Fri Sep 08 2017 - 02:32:50 CDT)
Re: Constraining and imparting motion to a geometry Abhaysinh Gaikwad (Thu Sep 07 2017 - 14:35:01 CDT)
Re: -nan values and fatal error Vermaas, Joshua (Thu Sep 07 2017 - 12:15:51 CDT)
-nan values and fatal error Natasha Gupta (Thu Sep 07 2017 - 11:24:29 CDT)
Re: No minimized system after running minimization in NAMD Ajasja LjubetiÄ (Thu Sep 07 2017 - 09:38:18 CDT)
No minimized system after running minimization in NAMD Roshan Shrestha (Thu Sep 07 2017 - 09:17:02 CDT)
Re: Concatenating log files Roshan Shrestha (Wed Sep 06 2017 - 12:00:34 CDT)
RE: Concatenating log files Bennion, Brian (Wed Sep 06 2017 - 11:50:53 CDT)
Re: Concatenating log files Roshan Shrestha (Wed Sep 06 2017 - 11:39:06 CDT)
Re: Concatenating log files Brian Radak (Wed Sep 06 2017 - 11:32:02 CDT)
Re: Concatenating log files Vermaas, Joshua (Wed Sep 06 2017 - 11:14:52 CDT)
Concatenating log files Roshan Shrestha (Wed Sep 06 2017 - 11:07:51 CDT)
Re: applying constant force on water molecules in a particular direction Giacomo Fiorin (Wed Sep 06 2017 - 07:08:34 CDT)
applying constant force on water molecules in a particular direction Sanjib Paul (Wed Sep 06 2017 - 06:14:16 CDT)
Too many iterations in routine jacobi during FEP Francesco Pietra (Wed Sep 06 2017 - 01:36:16 CDT)
Re: NAMD2.9-ERROR: Constraint failure in RATTLE algorithm for atom! çŽ‹èŒœèŒœ (Tue Sep 05 2017 - 05:23:02 CDT)
Re: How to set the configuration file for a NVE simulation Roshan Shrestha (Mon Sep 04 2017 - 19:59:40 CDT)
How to set the configuration file for a NVE simulation Monika Madhavi (Mon Sep 04 2017 - 19:02:29 CDT)
RFC: shell scripts and support functions for NAMD on Slurm (including GPU and Infiniband) Renfro, Michael (Mon Sep 04 2017 - 13:57:54 CDT)
Dihedral colvar PRITI ROY (Mon Sep 04 2017 - 06:08:00 CDT)
Re: QM atoms outside the PBC boundary in QM/MM calculation Haohao Fu (Sun Sep 03 2017 - 08:56:44 CDT)
QM atoms outside the PBC boundary in QM/MM calculation Haohao Fu (Sat Sep 02 2017 - 21:55:26 CDT)
FATAL ERROR: Singular matrix in routine ludcmp Natasha Gupta (Fri Sep 01 2017 - 18:41:24 CDT)
Re: Regular vs US sampling runs. jeevan gc (Fri Sep 01 2017 - 16:32:20 CDT)
Re: error - atom type not in psf Vermaas, Joshua (Fri Sep 01 2017 - 16:06:53 CDT)
Constraining and imparting motion to a geometry Abhaysinh Gaikwad (Fri Sep 01 2017 - 14:47:21 CDT)
Re: Regular vs US sampling runs. Vermaas, Joshua (Fri Sep 01 2017 - 11:53:11 CDT)
Re: error - atom type not in psf Vermaas, Joshua (Fri Sep 01 2017 - 11:36:19 CDT)
Re: Regular vs US sampling runs. jeevan gc (Fri Sep 01 2017 - 11:32:27 CDT)
Re: problem with minimization and calculation of force on a fixed atom JÃ©rÃ´me HÃ©nin (Fri Sep 01 2017 - 11:23:23 CDT)
Re: problem with minimization and calculation of force on a fixed atom JÃ©rÃ´me HÃ©nin (Fri Sep 01 2017 - 11:02:52 CDT)
Re: problem with minimization and calculation of force on a fixed atom Ben Adams (Fri Sep 01 2017 - 11:01:49 CDT)
Re: problem with minimization and calculation of force on a fixed atom JÃ©rÃ´me HÃ©nin (Fri Sep 01 2017 - 10:48:49 CDT)
Re: problem with minimization and calculation of force on a fixed atom Ben Adams (Fri Sep 01 2017 - 10:36:21 CDT)
AW: NAMD-2.12 CUDA2 and PMECUDA problems Norman Geist (Fri Sep 01 2017 - 03:23:28 CDT)
Re: error - atom type not in psf Natasha Gupta (Fri Sep 01 2017 - 02:28:46 CDT)
Re: Regular vs US sampling runs. Giacomo Fiorin (Thu Aug 31 2017 - 21:34:56 CDT)
Re: Regular vs US sampling runs. jeevan gc (Thu Aug 31 2017 - 20:13:38 CDT)
Re: Regular vs US sampling runs. Vermaas, Joshua (Thu Aug 31 2017 - 18:56:17 CDT)
Regular vs US sampling runs. jeevan gc (Thu Aug 31 2017 - 18:23:43 CDT)
Re: error - atom type not in psf Vermaas, Joshua (Thu Aug 31 2017 - 17:49:48 CDT)
Re: problem with minimization and calculation of force on a fixed atom JÃ©rÃ´me HÃ©nin (Thu Aug 31 2017 - 17:36:54 CDT)
problem with minimization and calculation of force on a fixed atom Ben Adams (Thu Aug 31 2017 - 17:03:21 CDT)
Re: error - atom type not in psf Vermaas, Joshua (Thu Aug 31 2017 - 11:25:10 CDT)
Proper combination of langevinHydrogen with rigidbonds Benjamin Rousseau (Thu Aug 31 2017 - 10:31:31 CDT)
Re: extracting force on a single atom Ben Adams (Thu Aug 31 2017 - 10:11:19 CDT)
Re: extracting force on a single atom Florian Blanc (Thu Aug 31 2017 - 10:07:59 CDT)
Re: extracting force on a single atom Ben Adams (Thu Aug 31 2017 - 10:03:04 CDT)
Re: extracting force on a single atom Ben Adams (Thu Aug 31 2017 - 08:38:05 CDT)
error - atom type not in psf Natasha Gupta (Thu Aug 31 2017 - 05:56:15 CDT)
Radial pair distribution function for internal water analysis James Starlight (Thu Aug 31 2017 - 05:49:39 CDT)
Re: calculate cumulative dG Nehad Elsalamouny (Wed Aug 30 2017 - 19:20:09 CDT)
extracting force on a single atom Ben Adams (Wed Aug 30 2017 - 19:18:49 CDT)
Re: NAMD-2.12 CUDA2 and PMECUDA problems David Hardy (Wed Aug 30 2017 - 11:05:47 CDT)
Re: vmd-l: 780Ti and NAMD2 David Hardy (Wed Aug 30 2017 - 10:21:40 CDT)
Re: Creating psf file DNA Vermaas, Joshua (Wed Aug 30 2017 - 10:11:27 CDT)
AW: AW: NAMD-2.12 CUDA2 and PMECUDA problems Norman Geist (Wed Aug 30 2017 - 03:47:53 CDT)
Re: AW: NAMD-2.12 CUDA2 and PMECUDA problems Nicholas M Glykos (Wed Aug 30 2017 - 03:05:17 CDT)
AW: NAMD-2.12 CUDA2 and PMECUDA problems Norman Geist (Wed Aug 30 2017 - 02:13:41 CDT)
Re: NAMD-2.12 CUDA2 and PMECUDA problems Nicholas M. Glykos (Tue Aug 29 2017 - 12:54:40 CDT)
Re: Steered Molecular Dynamics Abhaysinh Gaikwad (Tue Aug 29 2017 - 10:25:19 CDT)
Re: Production run after equilibration Brian Radak (Tue Aug 29 2017 - 10:10:44 CDT)
Re: calculate cumulative dG Brian Radak (Tue Aug 29 2017 - 10:08:25 CDT)
Production run after equilibration Roshan Shrestha (Tue Aug 29 2017 - 05:38:00 CDT)
calculate cumulative dG Nehad Elsalamouny (Tue Aug 29 2017 - 00:18:16 CDT)
Re: raising temperature after equiliobration Brian Radak (Mon Aug 28 2017 - 09:12:40 CDT)
NAMD-2.12 CUDA2 and PMECUDA problems Norman Geist (Mon Aug 28 2017 - 05:54:58 CDT)
AW: Movie in VMD Daniel MÃ¶ller (Sun Aug 27 2017 - 08:13:39 CDT)
Movie in VMD Daipayan Sarkar (Sat Aug 26 2017 - 22:56:24 CDT)
Re: Periodic cell too small with GPUs, not with pur CPUs JC Gumbart (Sat Aug 26 2017 - 08:11:13 CDT)
raising temperature after equiliobration t.shivam_at_iitg.ernet.in (Sat Aug 26 2017 - 02:20:20 CDT)
Re: NAMD2.9-ERROR: Constraint failure in RATTLE algorithm for atom! Richard (Fri Aug 25 2017 - 23:03:00 CDT)
NAMD2.9-ERROR: Constraint failure in RATTLE algorithm for atom! çŽ‹èŒœèŒœ (Fri Aug 25 2017 - 22:47:16 CDT)
NAMD2.9-ERROR: Constraint failure in RATTLE algorithm for atom! çŽ‹èŒœèŒœ (Fri Aug 25 2017 - 22:33:43 CDT)
Re: Periodic cell too small with GPUs, not with pur CPUs David Hardy (Fri Aug 25 2017 - 21:34:38 CDT)
Re: Periodic cell too small with GPUs, not with pur CPUs JC Gumbart (Fri Aug 25 2017 - 17:09:49 CDT)
Re: "Periodic cell has become too small for original patch grid!" with membrane system on GPU David Hardy (Fri Aug 25 2017 - 14:39:24 CDT)
Re: Periodic cell too small with GPUs, not with pur CPUs David Hardy (Fri Aug 25 2017 - 14:31:31 CDT)
Re: Steered Molecular Dynamics Bassam Haddad (Fri Aug 25 2017 - 12:38:14 CDT)
Re: make psf error for ligand Natasha Gupta (Fri Aug 25 2017 - 05:37:38 CDT)
Re: How to get the right density of a methane system Monika Madhavi (Fri Aug 25 2017 - 03:29:17 CDT)
Steered Molecular Dynamics Abhaysinh Gaikwad (Thu Aug 24 2017 - 13:28:49 CDT)
Re: make psf error for ligand Oscar Bastidas (Thu Aug 24 2017 - 13:26:58 CDT)
Re: Creating psf file for ligand JoÃ£o Ribeiro (Thu Aug 24 2017 - 13:19:32 CDT)
Re: Creating psf file for ligand Roshan Shrestha (Thu Aug 24 2017 - 12:58:07 CDT)
Re: make psf error for ligand Nikhil Maroli (Thu Aug 24 2017 - 12:44:45 CDT)
Re: Simulating Protein/Membrane interface with pre-equiliibrated lipid bilayer Vermaas, Joshua (Wed Aug 23 2017 - 19:16:51 CDT)
Simulating Protein/Membrane interface with pre-equiliibrated lipid bilayer Arthur Vale (Wed Aug 23 2017 - 18:58:59 CDT)
Re: make psf error for ligand Oscar Bastidas (Wed Aug 23 2017 - 17:59:27 CDT)
Re: error - parameter file for fluorine on a benzene ring Kowsar Khajeh (Wed Aug 23 2017 - 17:38:42 CDT)
Re: make psf error for ligand Natasha Gupta (Wed Aug 23 2017 - 17:35:34 CDT)
make psf error for ligand Natasha Gupta (Wed Aug 23 2017 - 16:46:55 CDT)
error - parameter file for fluorine on a benzene ring Natasha Gupta (Wed Aug 23 2017 - 15:07:08 CDT)
Re: Creating psf file for ligand Nikhil Maroli (Wed Aug 23 2017 - 10:07:59 CDT)
Re: Creating psf file for ligand Nikhil Maroli (Mon Aug 21 2017 - 12:33:07 CDT)
Issues about Keep_water_out.tcl acript Vidhya Sankar (Fri Aug 18 2017 - 10:25:55 CDT)
Re: NAMD with multiple molecules t.shivam_at_iitg.ernet.in (Thu Aug 17 2017 - 22:51:58 CDT)
Re: Software for molecular electrostatic calculations David Hardy (Thu Aug 17 2017 - 13:28:19 CDT)
Re: difference between .vel and .vel.restart David Hardy (Thu Aug 17 2017 - 13:25:02 CDT)
Re: NAMD with multiple molecules Axel Kohlmeyer (Thu Aug 17 2017 - 10:15:15 CDT)
NAMD with multiple molecules Benz, Max (Thu Aug 17 2017 - 10:09:17 CDT)
Reg membrane assembly Vidhya Sankar (Thu Aug 17 2017 - 00:37:42 CDT)
Re: restarting and continuing - difference Giacomo Fiorin (Mon Aug 14 2017 - 09:16:24 CDT)
restarting and continuing - difference t.shivam_at_iitg.ernet.in (Mon Aug 14 2017 - 09:05:03 CDT)
reg diffusion of water molecules Vidhya Sankar (Sat Aug 12 2017 - 23:51:25 CDT)
Re: replica_bias and colvars Giacomo Fiorin (Sat Aug 12 2017 - 13:29:48 CDT)
Re: Creating psf file for ligand Roshan Shrestha (Sat Aug 12 2017 - 09:38:59 CDT)
Creating psf file for ligand Roshan Shrestha (Sat Aug 12 2017 - 09:34:29 CDT)
Re: replica_bias and colvars JC Gumbart (Sat Aug 12 2017 - 06:49:35 CDT)
Re: How to get the right density of a methane system Francesco Pietra (Sat Aug 12 2017 - 01:07:54 CDT)
RE: How to get the right density of a methane system Nielsen, Steven (Fri Aug 11 2017 - 23:38:18 CDT)
How to get the right density of a methane system Monika Madhavi (Fri Aug 11 2017 - 21:56:51 CDT)
How to get 3D figure of solvent accessible surface area from APBS output Rabeta Yeasmin (Fri Aug 11 2017 - 17:18:54 CDT)
Re: simulation crashing in 2nd stage equilibration Giacomo Fiorin (Fri Aug 11 2017 - 08:31:53 CDT)
Re: simulation crashing in 2nd stage equilibration t.shivam_at_iitg.ernet.in (Fri Aug 11 2017 - 08:20:42 CDT)
Re: simulation crashing in 2nd stage equilibration Giacomo Fiorin (Fri Aug 11 2017 - 07:57:11 CDT)
simulation crashing in 2nd stage equilibration t.shivam_at_iitg.ernet.in (Fri Aug 11 2017 - 06:32:32 CDT)
Re: replica_bias and colvars Giacomo Fiorin (Thu Aug 10 2017 - 21:10:21 CDT)
Re: replica_bias and colvars JC Gumbart (Thu Aug 10 2017 - 16:17:21 CDT)
Re: replica_bias and colvars Giacomo Fiorin (Thu Aug 10 2017 - 15:25:35 CDT)
Re: ABF vs Umbrella Sampling entrance barrier heights discrepancy JÃ©rÃ´me HÃ©nin (Thu Aug 10 2017 - 14:11:42 CDT)
Re: replica_bias and colvars Vermaas, Joshua (Thu Aug 10 2017 - 12:58:27 CDT)
Re: replica_bias and colvars Giacomo Fiorin (Thu Aug 10 2017 - 12:51:26 CDT)
Re: ABF vs Umbrella Sampling entrance barrier heights discrepancy Olya Kravchenko (Thu Aug 10 2017 - 12:45:48 CDT)
replica_bias and colvars JC Gumbart (Thu Aug 10 2017 - 12:07:45 CDT)
Re: Software for molecular electrostatic calculations Rabeta Yeasmin (Thu Aug 10 2017 - 10:31:58 CDT)
Re: Software for molecular electrostatic calculations Giacomo Fiorin (Thu Aug 10 2017 - 08:15:28 CDT)
Re: value of langevinTemp in case of binvelocities t.shivam_at_iitg.ernet.in (Thu Aug 10 2017 - 04:41:10 CDT)
difference between .vel and .vel.restart t.shivam_at_iitg.ernet.in (Thu Aug 10 2017 - 04:39:49 CDT)
Re: value of langevinTemp in case of binvelocities fhh2626_at_gmail.com (Thu Aug 10 2017 - 02:13:20 CDT)
value of langevinTemp in case of binvelocities t.shivam_at_iitg.ernet.in (Thu Aug 10 2017 - 02:05:43 CDT)
Re: NAMD for Stampede2 Maria Bykhovskaia (Wed Aug 09 2017 - 20:21:20 CDT)
Re: NAMD for Stampede2 Vermaas, Joshua (Wed Aug 09 2017 - 17:45:00 CDT)
Re: TMD without alignment John Green (Wed Aug 09 2017 - 17:27:25 CDT)
Re: Software for molecular electrostatic calculations Rabeta Yeasmin (Wed Aug 09 2017 - 16:44:01 CDT)
Re: finding atoms in protein-lipid system having electrostatic interaction Giacomo Fiorin (Wed Aug 09 2017 - 14:19:26 CDT)
Re: Software for molecular electrostatic calculations Giacomo Fiorin (Wed Aug 09 2017 - 14:16:54 CDT)
finding atoms in protein-lipid system having electrostatic interaction Rabeta Yeasmin (Wed Aug 09 2017 - 13:32:35 CDT)
Software for molecular electrostatic calculations Rabeta Yeasmin (Wed Aug 09 2017 - 13:03:49 CDT)
Re: Coarse Grain of a Calcium Binding Protein Ajasja LjubetiÄ (Wed Aug 09 2017 - 10:51:34 CDT)
Coarse Grain of a Calcium Binding Protein Nisler, Collin R. (Wed Aug 09 2017 - 10:31:24 CDT)
NAMD for Stampede2 Maria Bykhovskaia (Wed Aug 09 2017 - 10:26:57 CDT)
Functional role of the internal water channel within the receptor James Starlight (Tue Aug 08 2017 - 07:42:07 CDT)
Re: Syntax for replicaRecv Florian Blanc (Tue Aug 08 2017 - 05:13:50 CDT)
Re: Syntax for replicaRecv Florian Blanc (Mon Aug 07 2017 - 08:47:02 CDT)
Re: difference between constraining,restraining and fixing the atoms JÃ©rÃ´me HÃ©nin (Sun Aug 06 2017 - 10:20:51 CDT)
Re: ABF vs Umbrella Sampling entrance barrier heights discrepancy JÃ©rÃ´me HÃ©nin (Sun Aug 06 2017 - 10:17:44 CDT)
Re: Are KNL a good choice for classical MD? Francesco Pietra (Sun Aug 06 2017 - 03:04:31 CDT)
Fwd: Are KNL a good choice for classical MD? Francesco Pietra (Sat Aug 05 2017 - 02:42:31 CDT)
Re: Are KNL a good choice for classical MD? Francesco Pietra (Sat Aug 05 2017 - 02:02:09 CDT)
Re: Are KNL a good choice for classical MD? Vermaas, Joshua (Fri Aug 04 2017 - 16:34:28 CDT)
Are KNL a good choice for classical MD? Francesco Pietra (Fri Aug 04 2017 - 15:51:48 CDT)
TMD without alignment John Green (Fri Aug 04 2017 - 13:27:31 CDT)
Problem in running wham Rabeta Yeasmin (Fri Aug 04 2017 - 10:41:06 CDT)
Syntax for replicaRecv Florian Blanc (Fri Aug 04 2017 - 10:17:27 CDT)
Re: difference between constraining,restraining and fixing the atoms Brian Radak (Fri Aug 04 2017 - 09:34:22 CDT)
Re: Periodic cell too small with GPUs, not with pur CPUs Francesco Pietra (Fri Aug 04 2017 - 06:44:37 CDT)
Re: difference between constraining,restraining and fixing the atoms Fotis Baltoumas (Thu Aug 03 2017 - 23:33:22 CDT)
difference between constraining,restraining and fixing the atoms t.shivam_at_iitg.ernet.in (Fri Aug 04 2017 - 01:25:23 CDT)
Re: Setting up softcore parameters for FEP Brian Radak (Thu Aug 03 2017 - 13:03:29 CDT)
Re: ABF for dihedrals Giacomo Fiorin (Thu Aug 03 2017 - 12:53:19 CDT)
Re: Setting up softcore parameters for FEP John Green (Thu Aug 03 2017 - 12:49:20 CDT)
ABF for dihedrals Albers, Thomas (Thu Aug 03 2017 - 12:48:24 CDT)
Re: two stage equilibration in single configuration file Brian Radak (Thu Aug 03 2017 - 12:45:14 CDT)
Re: two stage equilibration in single configuration file Bassam Haddad (Thu Aug 03 2017 - 12:29:53 CDT)
Re: Setting up softcore parameters for FEP Brian Radak (Thu Aug 03 2017 - 12:02:47 CDT)
Re: Namd 2.12 error with Nvidia M2090 cards Vermaas, Joshua (Thu Aug 03 2017 - 11:45:40 CDT)
Re: Setting up softcore parameters for FEP John Green (Thu Aug 03 2017 - 11:38:37 CDT)
Re: two stage equilibration in single configuration file Vermaas, Joshua (Thu Aug 03 2017 - 11:38:18 CDT)
Re: Setting up softcore parameters for FEP Brian Radak (Thu Aug 03 2017 - 08:20:36 CDT)
Namd 2.12 error with Nvidia M2090 cards Michelle Kuttel (Thu Aug 03 2017 - 03:30:21 CDT)
two stage equilibration in single configuration file t.shivam_at_iitg.ernet.in (Thu Aug 03 2017 - 01:03:46 CDT)
Q=9B=9E=E5=A4=8D:__Free_energy_(eABF):_ne?= gative RMSD and harmonic restraints. yjcoshc_at_gmail.com (Wed Aug 02 2017 - 20:00:22 CDT)
Setting up softcore parameters for FEP John Green (Wed Aug 02 2017 - 16:18:32 CDT)
ABF vs Umbrella Sampling entrance barrier heights discrepancy Olya Kravchenko (Wed Aug 02 2017 - 13:39:16 CDT)
Free energy (eABF): negative RMSD and harmonic restraints. philippe Bourly (Wed Aug 02 2017 - 11:45:56 CDT)
Re: Configuration of new HPC Cluster for NAMD and GROMACS Vogel, Alexander (Tue Aug 01 2017 - 05:45:57 CDT)
Re: Configuration of new HPC Cluster for NAMD and GROMACS Vermaas, Joshua (Mon Jul 31 2017 - 13:57:50 CDT)
Configuration of new HPC Cluster for NAMD and GROMACS Vogel, Alexander (Mon Jul 31 2017 - 05:36:30 CDT)
Re: How to calculate free energy to unbias colvars restraint? Giacomo Fiorin (Sat Jul 29 2017 - 09:51:01 CDT)
Re: How to calculate free energy to unbias colvars restraint? Victoria Lim (Fri Jul 28 2017 - 19:17:33 CDT)
Re: How to calculate free energy to unbias colvars restraint? Giacomo Fiorin (Fri Jul 28 2017 - 19:10:59 CDT)
How to calculate free energy to unbias colvars restraint? Victoria Lim (Fri Jul 28 2017 - 18:56:44 CDT)
Re: PACE CG Model Giacomo Fiorin (Fri Jul 28 2017 - 13:23:43 CDT)
PACE CG Model Alexander Adams (Fri Jul 28 2017 - 12:53:24 CDT)
Re: Running NAMD on Intel OmniPath David Hardy (Fri Jul 28 2017 - 10:29:37 CDT)
Re: Running NAMD on Intel OmniPath Giacomo Fiorin (Thu Jul 27 2017 - 17:53:52 CDT)
Re: Running NAMD on Intel OmniPath David Hardy (Thu Jul 27 2017 - 16:36:47 CDT)
Re: Problems running FEP on Lenovo NextScale KNL Brian Radak (Thu Jul 27 2017 - 15:55:21 CDT)
Re: Running NAMD on Intel OmniPath Giacomo Fiorin (Thu Jul 27 2017 - 14:33:38 CDT)
Re: Running NAMD on Intel OmniPath David Hardy (Thu Jul 27 2017 - 14:18:47 CDT)
Re: Running NAMD on Intel OmniPath Maxime Boissonneault (Thu Jul 27 2017 - 13:47:54 CDT)
Re: Running NAMD on Intel OmniPath Mauro Lapelosa (Thu Jul 27 2017 - 13:06:24 CDT)
Running NAMD on Intel OmniPath Maxime Boissonneault (Thu Jul 27 2017 - 13:00:04 CDT)
Does FEP really run on Knights Landing? Francesco Pietra (Thu Jul 27 2017 - 11:44:13 CDT)
Re: polymer Giacomo Fiorin (Thu Jul 27 2017 - 08:14:01 CDT)
polymer Nehir NALINCI (Thu Jul 27 2017 - 03:02:49 CDT)
Re: Problems running FEP on Lenovo NextScale KNL Francesco Pietra (Thu Jul 27 2017 - 01:27:24 CDT)
Re: Problems running FEP on Lenovo NextScale KNL Brian Radak (Wed Jul 26 2017 - 14:45:22 CDT)
Re: Problems running FEP on Lenovo NextScale KNL Francesco Pietra (Wed Jul 26 2017 - 10:27:20 CDT)
Re: Problems running FEP on Lenovo NextScale KNL Brian Radak (Wed Jul 26 2017 - 10:04:22 CDT)
Problems running FEP on Lenovo NextScale KNL Francesco Pietra (Wed Jul 26 2017 - 09:23:19 CDT)
Re: Re: I don't have any eabf output file. fhh2626_at_gmail.com (Wed Jul 26 2017 - 01:47:09 CDT)
Re: Re: I don't have any eabf output file. philippe Bourly (Tue Jul 25 2017 - 07:23:34 CDT)
Re: Re: I don't have any eabf output file. Haohao (Tue Jul 25 2017 - 06:20:33 CDT)
Re: Re: I don't have any eabf output file. Haohao (Tue Jul 25 2017 - 06:14:48 CDT)
Re: I don't have any eabf output file. philippe Bourly (Tue Jul 25 2017 - 05:20:51 CDT)
Re: I don't have any eabf output file. yjcoshc_at_gmail.com (Tue Jul 25 2017 - 05:06:44 CDT)
making glucose chains using charmm36 Mohammad Hassan Khatami (Mon Jul 24 2017 - 13:29:18 CDT)
Re: Too many iterations in routine jacobi. Francesco Pietra (Sun Jul 23 2017 - 01:58:42 CDT)
I don't have any eabf output file. philippe Bourly (Fri Jul 21 2017 - 13:46:39 CDT)
Re: eABF - Fullsamples and windows merging philippe Bourly (Fri Jul 21 2017 - 12:54:03 CDT)
Re: Too many iterations in routine jacobi. Giacomo Fiorin (Fri Jul 21 2017 - 12:49:56 CDT)
Re: Compiling NAMD on stampede 2. Giacomo Fiorin (Fri Jul 21 2017 - 12:47:07 CDT)
Re: Compiling NAMD on stampede 2. Chitrak Gupta (Fri Jul 21 2017 - 12:20:38 CDT)
Too many iterations in routine jacobi. Francesco Pietra (Fri Jul 21 2017 - 12:06:45 CDT)
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG321 CTL3 (ATOMS 8773 8776) Arthur Vale (Thu Jul 20 2017 - 20:08:28 CDT)
Re: Compiling NAMD on stampede 2. Giacomo Fiorin (Thu Jul 20 2017 - 11:45:18 CDT)
Re: Compiling NAMD on stampede 2. Chitrak Gupta (Thu Jul 20 2017 - 11:29:37 CDT)
Re: Compiling NAMD on stampede 2. Giacomo Fiorin (Thu Jul 20 2017 - 11:20:29 CDT)
Re: Compiling NAMD on stampede 2. Chitrak Gupta (Thu Jul 20 2017 - 11:09:29 CDT)
"Periodic cell has become too small for original patch grid!" with membrane system on GPU James Starlight (Thu Jul 20 2017 - 06:03:29 CDT)
Re: Compiling NAMD on stampede 2. Giacomo Fiorin (Wed Jul 19 2017 - 20:14:30 CDT)
Compiling NAMD on stampede 2. Chitrak Gupta (Wed Jul 19 2017 - 17:47:07 CDT)
Re: eABF - Fullsamples and windows merging yjcoshc_at_gmail.com (Wed Jul 19 2017 - 09:01:40 CDT)
eABF - Fullsamples and windows merging philippe Bourly (Wed Jul 19 2017 - 08:41:56 CDT)
Re: Periodic cell too small with GPUs, not with pur CPUs David Hardy (Tue Jul 18 2017 - 17:05:00 CDT)
Re: NAMD 2.12 multicore CUDA on Ubuntu 16.04 with NVIDIA Tesla M10 produces segmentation fault Wilson,Michael (Tue Jul 18 2017 - 15:18:28 CDT)
Re: NAMD 2.12 multicore CUDA on Ubuntu 16.04 with NVIDIA Tesla M10 produces segmentation fault Vermaas, Joshua (Tue Jul 18 2017 - 14:10:20 CDT)
NAMD 2.12 multicore CUDA on Ubuntu 16.04 with NVIDIA Tesla M10 produces segmentation fault Wilson,Michael (Tue Jul 18 2017 - 13:57:16 CDT)
Re: Error in thermodynamic integration for calculating ligand absolute binding free energy Brian Radak (Mon Jul 17 2017 - 15:55:21 CDT)
"Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL JoÃ£o Ribeiro (Mon Jul 17 2017 - 14:45:43 CDT)
Re: Simulation of the mechanical stress in NAMD Giacomo Fiorin (Mon Jul 17 2017 - 13:15:14 CDT)
Error in thermodynamic integration for calculating ligand absolute binding free energy Marawan Hussien (Mon Jul 17 2017 - 11:45:22 CDT)
Re: Periodic cell too small with GPUs, not with pur CPUs Francesco Pietra (Mon Jul 17 2017 - 09:09:20 CDT)
Re: Simulation of the mechanical stress in NAMD Giacomo Fiorin (Mon Jul 17 2017 - 07:49:49 CDT)
Simulation of the mechanical stress in NAMD James Starlight (Mon Jul 17 2017 - 02:55:30 CDT)
Re: ABF: umbrella_int.awk Francesco Pietra (Sat Jul 15 2017 - 08:45:00 CDT)
Re: Querries on eABF Souvik Sinha (Sat Jul 15 2017 - 07:39:34 CDT)
Re: ABF: umbrella_int.awk Giacomo Fiorin (Sat Jul 15 2017 - 07:04:13 CDT)
Re: ABF: umbrella_int.awk yjcoshc_at_gmail.com (Sat Jul 15 2017 - 07:02:33 CDT)
Re: ABF: umbrella_int.awk Francesco Pietra (Sat Jul 15 2017 - 03:36:33 CDT)
Re: ABF: umbrella_int.awk Giacomo Fiorin (Fri Jul 14 2017 - 08:21:10 CDT)
Re: ABF: umbrella_int.awk Giacomo Fiorin (Fri Jul 14 2017 - 08:20:15 CDT)
Re: ABF: umbrella_int.awk Francesco Pietra (Fri Jul 14 2017 - 03:39:48 CDT)
Re: Maintaining PBC on Collective Variables Malay Ranjan Biswal (Thu Jul 13 2017 - 11:49:15 CDT)
ABF: umbrella_int.awk Francesco Pietra (Thu Jul 13 2017 - 10:32:40 CDT)
Re: Querries on eABF Souvik Sinha (Wed Jul 12 2017 - 07:34:46 CDT)
Re: Querries on eABF Souvik Sinha (Wed Jul 12 2017 - 07:15:51 CDT)
Re: ABF FEP with multichain receptor Francesco Pietra (Tue Jul 11 2017 - 11:28:48 CDT)
Protein trapped on an edge of the simulation cell using C36 force field istamkos_at_auth.gr (Tue Jul 11 2017 - 03:15:51 CDT)
Fwd: ABF FEP with multichain receptor Francesco Pietra (Tue Jul 11 2017 - 01:20:12 CDT)
Re: Collective variable remains at zero during Umbrella Sampling Giacomo Fiorin (Mon Jul 10 2017 - 21:46:53 CDT)
Re: Maintaining PBC on Collective Variables Vermaas, Joshua (Mon Jul 10 2017 - 12:49:11 CDT)
Maintaining PBC on Collective Variables Malay Ranjan Biswal (Mon Jul 10 2017 - 08:17:30 CDT)
GAAMP Stefano Guglielmo (Mon Jul 10 2017 - 06:55:21 CDT)
Fwd: ABF FEP with multichain receptor Francesco Pietra (Mon Jul 10 2017 - 05:25:30 CDT)
Collective variable remains at zero during Umbrella Sampling Hemanth Vemuri (Sun Jul 09 2017 - 23:59:18 CDT)
Re: ABF FEP with multichain receptor Francesco Pietra (Sun Jul 09 2017 - 00:44:14 CDT)
Re: ABF FEP with multichain receptor Francesco Pietra (Sat Jul 08 2017 - 11:08:41 CDT)
Re: Cross-term (CMAP) Faramarz Joodaki (Sat Jul 08 2017 - 07:25:27 CDT)
Cross-term (CMAP) Faramarz Joodaki (Fri Jul 07 2017 - 18:04:48 CDT)
Re: Lipid_bilayer_area_per_lipid_problem_using_NPT_CharmmForcefield yousef nademi (Fri Jul 07 2017 - 17:50:40 CDT)
Water permeation through aquaporin-Z Isaac Twelves (Fri Jul 07 2017 - 13:04:37 CDT)
ABF FEP with multichain receptor Francesco Pietra (Fri Jul 07 2017 - 10:21:52 CDT)
Re: How to set setting periodic boundary condition Chitrak Gupta (Fri Jul 07 2017 - 09:54:54 CDT)
Re: Lipid_bilayer_area_per_lipid_problem_using_NPT_CharmmForcefield Fotis Baltoumas (Fri Jul 07 2017 - 02:22:06 CDT)
Re: Calculating electrostatic force from NAMD trajectory Ben Lowe (Fri Jul 07 2017 - 02:14:30 CDT)
Lipid_bilayer_area_per_lipid_problem_using_NPT_CharmmForcefield yousef nademi (Thu Jul 06 2017 - 20:49:48 CDT)
Re: Creating psf file DNA Vermaas, Joshua (Thu Jul 06 2017 - 18:02:37 CDT)
Re: Creating psf file DNA Roshan Shrestha (Thu Jul 06 2017 - 17:53:51 CDT)
Re: Creating psf file DNA Vermaas, Joshua (Thu Jul 06 2017 - 12:33:05 CDT)
Creating psf file DNA Roshan Shrestha (Thu Jul 06 2017 - 11:47:54 CDT)
How to set setting periodic boundary condition Vidhya Sankar (Thu Jul 06 2017 - 07:43:56 CDT)
Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Thu Jul 06 2017 - 01:15:50 CDT)
Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Giacomo Fiorin (Wed Jul 05 2017 - 11:30:59 CDT)
Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Wed Jul 05 2017 - 11:03:05 CDT)
Re: Periodic cell too small with GPUs, not with pur CPUs David Hardy (Wed Jul 05 2017 - 11:02:14 CDT)
Re: Periodic cell too small with GPUs, not with pur CPUs Joshua . (Wed Jul 05 2017 - 09:39:40 CDT)
Periodic cell too small with GPUs, not with pur CPUs Francesco Pietra (Wed Jul 05 2017 - 02:09:14 CDT)
Protein trapped on an edge of the simulation cell using C36 force field istamkos_at_auth.gr (Tue Jul 04 2017 - 01:25:13 CDT)
Re: Calculating electrostatic force from NAMD trajectory sunyeping (Mon Jul 03 2017 - 21:42:56 CDT)
Calculating electrostatic force from NAMD trajectory Ben Lowe (Mon Jul 03 2017 - 21:35:50 CDT)
Enhanced sampling of domain motion and gsafold dhirajks_at_gmail.com (Mon Jul 03 2017 - 19:18:38 CDT)
Fwd: enhanced sampling of domain motion, GSAfold Dhiraj Srivastava (Mon Jul 03 2017 - 16:33:17 CDT)
NAMD on UCSD Comet Alexander Adams (Mon Jul 03 2017 - 13:26:48 CDT)
write first point into (vel)dcd file Laura Joana (Mon Jul 03 2017 - 07:11:37 CDT)
Re: veldcdfile command Laura Joana (Mon Jul 03 2017 - 06:13:06 CDT)
enhanced sampling of domain motion, GSAfold Dhiraj Srivastava (Sat Jul 01 2017 - 23:49:00 CDT)
Re: Simulating SDS molecules Giacomo Fiorin (Fri Jun 30 2017 - 09:27:36 CDT)
Re: Simulating SDS molecules Ajasja LjubetiÄ (Fri Jun 30 2017 - 09:20:08 CDT)
Simulating SDS molecules Siddharth Girdhar (Fri Jun 30 2017 - 09:11:08 CDT)
Re: veldcdfile command Laura Joana (Fri Jun 30 2017 - 07:38:02 CDT)
Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Thu Jun 29 2017 - 08:47:59 CDT)
Re: veldcdfile command Laura Joana (Wed Jun 28 2017 - 14:26:17 CDT)
Re: veldcdfile command Laura Joana (Wed Jun 28 2017 - 14:25:35 CDT)
Re: veldcdfile command Giacomo Fiorin (Wed Jun 28 2017 - 13:36:43 CDT)
Re: veldcdfile command Laura Joana (Wed Jun 28 2017 - 13:09:28 CDT)
Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Giacomo Fiorin (Wed Jun 28 2017 - 11:35:19 CDT)
veldcdfile command Laura Joana (Wed Jun 28 2017 - 09:59:45 CDT)
Fwd: About the robustness of ABF and FEB protein-ligand Francesco Pietra (Wed Jun 28 2017 - 09:47:59 CDT)
About the robustness of ABF and FEB protein-ligand Francesco Pietra (Wed Jun 28 2017 - 09:40:15 CDT)
"Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL JoÃ£o Ribeiro (Tue Jun 27 2017 - 13:46:57 CDT)
Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Tue Jun 27 2017 - 02:46:38 CDT)
Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Giacomo Fiorin (Mon Jun 26 2017 - 11:32:58 CDT)
Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Mon Jun 26 2017 - 11:24:59 CDT)
Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Mon Jun 26 2017 - 05:28:49 CDT)
Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Sun Jun 25 2017 - 05:56:01 CDT)
Fwd: measuring Euler angles and polar angles Francesco Pietra (Sat Jun 24 2017 - 01:22:17 CDT)
Re: topology file for the residue CSO Radak, Brian K (Fri Jun 23 2017 - 13:10:51 CDT)
Re: measuring Euler angles and polar angles Francesco Pietra (Fri Jun 23 2017 - 12:06:18 CDT)
topology file for the residue CSO Hyun (Fri Jun 23 2017 - 11:43:38 CDT)
Re: measuring Euler angles and polar angles Giacomo Fiorin (Fri Jun 23 2017 - 10:00:36 CDT)
Re: measuring Euler angles and polar angles Francesco Pietra (Fri Jun 23 2017 - 09:55:31 CDT)
Re: REG Protein inserion in to membrane bi layear Vermaas, Joshua (Thu Jun 22 2017 - 12:25:00 CDT)
Re: measuring Euler angles and polar angles Giacomo Fiorin (Thu Jun 22 2017 - 12:18:00 CDT)
measuring Euler angles and polar angles Francesco Pietra (Thu Jun 22 2017 - 12:01:39 CDT)
RE: REG Protein inserion in to membrane bi layear Arthur Oliveira Vale (Thu Jun 22 2017 - 10:27:47 CDT)
Re: Defining custom Colvars to measure pmf with Umbrella Sampling Giacomo Fiorin (Thu Jun 22 2017 - 09:15:21 CDT)
Re: Defining custom Colvars to measure pmf with Umbrella Sampling Hemanth Vemuri (Thu Jun 22 2017 - 01:34:15 CDT)
Re: Defining custom Colvars to measure pmf with Umbrella Sampling Hemanth Vemuri (Thu Jun 22 2017 - 00:26:31 CDT)
Re: Harmonic force Keyword "centers" significance Vermaas, Joshua (Wed Jun 21 2017 - 17:49:20 CDT)
Harmonic force Keyword "centers" significance Rabeta Yeasmin (Wed Jun 21 2017 - 17:40:43 CDT)
Re: Defining custom Colvars to measure pmf with Umbrella Sampling Radak, Brian K (Wed Jun 21 2017 - 11:16:49 CDT)
Re: Defining custom Colvars to measure pmf with Umbrella Sampling Vermaas, Joshua (Wed Jun 21 2017 - 11:06:57 CDT)
Re: Defining custom Colvars to measure pmf with Umbrella Sampling Radak, Brian K (Wed Jun 21 2017 - 11:01:08 CDT)
Re: run namd cuda with srun. FÄ±rat YÄ±lmaz (Wed Jun 21 2017 - 03:36:09 CDT)
AW: Organic Solvent & Water Simulation Norman Geist (Wed Jun 21 2017 - 02:31:42 CDT)
Re: Defining custom Colvars to measure pmf with Umbrella Sampling Giacomo Fiorin (Tue Jun 20 2017 - 21:49:26 CDT)
run namd cuda with srun. FÄ±rat YÄ±lmaz (Tue Jun 20 2017 - 16:03:29 CDT)
Organic Solvent & Water Simulation Oscar Bastidas (Tue Jun 20 2017 - 15:15:05 CDT)
Reg seeting of periodic boundary condition Vidhya Sankar (Tue Jun 20 2017 - 11:56:59 CDT)
Re: REG Protein inserion in to membrane bi layear Vermaas, Joshua (Tue Jun 20 2017 - 10:49:51 CDT)
REG Protein inserion in to membrane bi layear Vidhya Sankar (Tue Jun 20 2017 - 05:05:39 CDT)
Defining custom Colvars to measure pmf with Umbrella Sampling Hemanth Vemuri (Tue Jun 20 2017 - 00:25:29 CDT)
Re: Simulating Protein Entering membrane Vermaas, Joshua (Mon Jun 19 2017 - 12:01:45 CDT)
Re: GaMD in NAMD Chitrak Gupta (Mon Jun 19 2017 - 08:43:37 CDT)
Re: GaMD in NAMD Francesco Pietra (Mon Jun 19 2017 - 00:36:19 CDT)
Simulating Protein Entering membrane Arthur Oliveira Vale (Sun Jun 18 2017 - 20:14:32 CDT)
Re: [NAMD] How to build and simulate a periodic DNA in NAMD The Cromicus Productions (Sun Jun 18 2017 - 17:47:39 CDT)
Re: GaMD in NAMD Chitrak Gupta (Sun Jun 18 2017 - 14:57:20 CDT)
Re: GaMD in NAMD David Hardy (Sun Jun 18 2017 - 11:02:19 CDT)
Re: GaMD in NAMD jeevan gc (Sun Jun 18 2017 - 10:49:40 CDT)
Re: GaMD in NAMD Chitrak Gupta (Sun Jun 18 2017 - 09:20:11 CDT)
Re: GaMD in NAMD Francesco Pietra (Sun Jun 18 2017 - 01:04:59 CDT)
GaMD in NAMD Chitrak Gupta (Sat Jun 17 2017 - 15:16:18 CDT)
Setting up the range for movement of protein in umbrella sampling Rabeta Yeasmin (Fri Jun 16 2017 - 16:21:55 CDT)
missing binary operator before token "(" FÄ±rat YÄ±lmaz (Thu Jun 15 2017 - 02:30:12 CDT)
Re: Gyration in colvars doesn't work with eABF. Haohao Fu (Thu Jun 15 2017 - 02:17:55 CDT)
Reg seeting of periodic boundary condition Vidhya Sankar (Wed Jun 14 2017 - 21:59:27 CDT)
Re: Questions on implementing new collective variable in colvars. JÃ©rÃ´me HÃ©nin (Wed Jun 14 2017 - 07:26:16 CDT)
Gyration in colvars doesn't work with eABF. yjcoshc (Wed Jun 14 2017 - 06:49:51 CDT)
principal axes in colvars Stefano Guglielmo (Wed Jun 14 2017 - 06:28:44 CDT)
Re: Two parameter file in NAMD configuration file divyabharathi korlepara (Wed Jun 14 2017 - 00:01:04 CDT)
Re: Questions on implementing new collective variable in colvars. yjcoshc (Tue Jun 13 2017 - 20:36:32 CDT)
Re: How to pull protein-Monomer from DNA using ABF without any force on DNA? Jeff Comer (Tue Jun 13 2017 - 13:37:05 CDT)
How to pull protein-Monomer from DNA using ABF without any force on DNA? Mehdi Bagherpour (Tue Jun 13 2017 - 12:30:29 CDT)
Re: [NAMD] How to build and simulate a periodic DNA in NAMD Vermaas, Joshua (Tue Jun 13 2017 - 12:09:32 CDT)
Re: Questions on implementing new collective variable in colvars. JÃ©rÃ´me HÃ©nin (Tue Jun 13 2017 - 10:32:23 CDT)
Re: [NAMD] How to build and simulate a periodic DNA in NAMD The Cromicus Productions (Tue Jun 13 2017 - 05:42:00 CDT)
Re: Questions on implementing new collective variable in colvars. yjcoshc (Mon Jun 12 2017 - 22:48:26 CDT)
Re: Questions on implementing new collective variable in colvars. Axel Kohlmeyer (Mon Jun 12 2017 - 22:38:48 CDT)
Questions on implementing new collective variable in colvars. yjcoshc (Mon Jun 12 2017 - 22:14:35 CDT)
Re: FEP with ExtraBonds Radak, Brian K (Mon Jun 12 2017 - 16:13:31 CDT)
FEP with ExtraBonds Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Mon Jun 12 2017 - 15:30:59 CDT)
Re: Two parameter file in NAMD configuration file Vermaas, Joshua (Mon Jun 12 2017 - 10:20:44 CDT)
Re: Converting x,y,z coordinates to dcd file Vermaas, Joshua (Mon Jun 12 2017 - 10:17:24 CDT)
Converting x,y,z coordinates to dcd file Kashish Punjani (Sun Jun 11 2017 - 12:44:18 CDT)
Re: Re: namd-l digest V1 #2196 Vermaas, Joshua (Fri Jun 09 2017 - 17:07:05 CDT)
Re: namd-l digest V1 #2196 Rabeta Yeasmin (Fri Jun 09 2017 - 15:40:37 CDT)
Re: [NAMD] How to build and simulate a periodic DNA in NAMD Vermaas, Joshua (Fri Jun 09 2017 - 12:42:49 CDT)
Re: [NAMD] How to build and simulate a periodic DNA in NAMD The Cromicus Productions (Fri Jun 09 2017 - 12:31:08 CDT)
Re: Two parameter file in NAMD configuration file Vermaas, Joshua (Fri Jun 09 2017 - 12:00:01 CDT)
Re: coarse-grained simulations with errors "Atoms moving too fast" and "low global exclusion" Yaxin An (Fri Jun 09 2017 - 10:38:33 CDT)
Re: coarse-grained simulations with errors "Atoms moving too fast" and "low global exclusion" Peter Freddolino (Fri Jun 09 2017 - 10:10:21 CDT)
Re: coarse-grained simulations with errors "Atoms moving too fast" and "low global exclusion" Richard Overstreet (Fri Jun 09 2017 - 09:45:06 CDT)
Re: Two parameter file in NAMD configuration file Radak, Brian K (Fri Jun 09 2017 - 09:39:46 CDT)
coarse-grained simulations with errors "Atoms moving too fast" and "low global exclusion" Yaxin An (Fri Jun 09 2017 - 09:39:28 CDT)
Two parameter file in NAMD configuration file divyabharathi korlepara (Fri Jun 09 2017 - 02:58:16 CDT)
NAMD DCD file format Dmitri Priimak (Fri Jun 09 2017 - 01:47:36 CDT)
Re: Colvars wall boundaries for CoordNum Giacomo Fiorin (Thu Jun 08 2017 - 19:42:46 CDT)
Colvars wall boundaries for CoordNum Wasut Pornpatcharapong (Thu Jun 08 2017 - 19:27:50 CDT)
Re: Umbrella Sampling colvar file parameters Vermaas, Joshua (Thu Jun 08 2017 - 12:32:44 CDT)
Umbrella Sampling colvar file parameters Rabeta Yeasmin (Thu Jun 08 2017 - 12:20:16 CDT)
Re: Keeping potassium ions out of an area during equilibration Vermaas, Joshua (Wed Jun 07 2017 - 12:15:45 CDT)
Restraining the mass centre coordinate during Umbrella Sampling Rabeta Yeasmin (Wed Jun 07 2017 - 10:46:57 CDT)
Re: Keeping potassium ions out of an area during equilibration Souvik Sinha (Wed Jun 07 2017 - 01:37:38 CDT)
Restring the coordinate during Umbrella Sampling Rabeta Yeasmin (Tue Jun 06 2017 - 16:13:08 CDT)
Re: Segmentation fault error with 'nan' pressure and energy Sadegh Faramarzi Ganjabad (Tue Jun 06 2017 - 14:07:24 CDT)
Re: Keeping potassium ions out of an area during equilibration Vermaas, Joshua (Tue Jun 06 2017 - 11:59:46 CDT)
Re: about GaMD reweighting Radak, Brian K (Tue Jun 06 2017 - 11:29:09 CDT)
about GaMD reweighting Francesco Pietra (Tue Jun 06 2017 - 10:58:40 CDT)
Keeping potassium ions out of an area during equilibration Charles Hoying (Mon Jun 05 2017 - 22:57:40 CDT)
Re: Center of mass drift M. Wong (Sat Jun 03 2017 - 04:44:18 CDT)
Re: Center of mass drift David Hardy (Fri Jun 02 2017 - 12:35:12 CDT)
RE: Center of mass drift Radak, Brian K (Fri Jun 02 2017 - 10:10:01 CDT)
Re: DNA capping Strahs, Dr. Daniel Bernard (Fri Jun 02 2017 - 10:01:52 CDT)
Re: DNA capping Nicholus Bhattacharjee (Fri Jun 02 2017 - 09:57:41 CDT)
RE: DNA capping Lennart Nilsson (Fri Jun 02 2017 - 09:10:04 CDT)
Re: DNA capping Nicholus Bhattacharjee (Fri Jun 02 2017 - 07:38:24 CDT)
Re: DNA capping Strahs, Dr. Daniel Bernard (Fri Jun 02 2017 - 07:30:57 CDT)
Re: DNA capping Nicholus Bhattacharjee (Fri Jun 02 2017 - 07:09:08 CDT)
Center of mass drift M. Wong (Fri Jun 02 2017 - 04:10:50 CDT)
Re: Segmentation fault error with 'nan' pressure and energy Sadegh Faramarzi Ganjabad (Thu Jun 01 2017 - 13:05:09 CDT)
DNA capping Nicholus Bhattacharjee (Thu Jun 01 2017 - 04:11:48 CDT)
Re: Segmentation fault error with 'nan' pressure and energy Brian Radak (Wed May 31 2017 - 18:24:19 CDT)
Re: Re: Segmentation fault error with 'nan' pressure and energy Sadegh Faramarzi Ganjabad (Wed May 31 2017 - 13:37:09 CDT)
Problem with running on multiple nodes Karteek Bejagam (Wed May 31 2017 - 11:33:48 CDT)
Re: Fatal error in the simulation of a water box Brian Radak (Wed May 31 2017 - 08:33:47 CDT)
Fatal error in the simulation of a water box M. Wong (Wed May 31 2017 - 04:04:38 CDT)
Re: Querries on eABF yjcoshc_at_gmail.com (Tue May 30 2017 - 20:18:40 CDT)
Re: Segmentation fault error with 'nan' pressure and energy Vermaas, Joshua (Tue May 30 2017 - 17:14:16 CDT)
Re: Segmentation fault error with 'nan' pressure and energy Sadegh Faramarzi Ganjabad (Tue May 30 2017 - 16:48:09 CDT)
Re: Segmentation fault error with 'nan' pressure and energy Richard Overstreet (Tue May 30 2017 - 16:41:33 CDT)
Segmentation fault error with 'nan' pressure and energy Sadegh Faramarzi Ganjabad (Tue May 30 2017 - 16:17:12 CDT)
Re: pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Tue May 30 2017 - 13:12:23 CDT)
Re: NAMD crashes when Multilevel Summation Method (MSM) is on David Hardy (Tue May 30 2017 - 11:11:07 CDT)
Re: Querries on eABF Souvik Sinha (Tue May 30 2017 - 11:01:09 CDT)
NAMD crashes when Multilevel Summation Method (MSM) is on Shadrina Maria (Tue May 30 2017 - 10:12:46 CDT)
Re: pKa calculation with thermodynamic integration (TI) Brian Radak (Tue May 30 2017 - 09:23:34 CDT)
Re: Querries on eABF Giacomo Fiorin (Tue May 30 2017 - 08:12:30 CDT)
Re: Querries on eABF Souvik Sinha (Tue May 30 2017 - 07:37:19 CDT)
Re: Querries on eABF Souvik Sinha (Tue May 30 2017 - 02:51:31 CDT)
Re: pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Mon May 29 2017 - 15:45:10 CDT)
Re: Error regarding missing angles between perturbed groups for fep calculation Vermaas, Joshua (Fri May 26 2017 - 17:09:53 CDT)
RE: Error regarding missing angles between perturbed groups for fep calculation Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Fri May 26 2017 - 17:03:36 CDT)
Re: Querries on eABF Souvik Sinha (Fri May 26 2017 - 10:53:04 CDT)
Re: Querries on eABF Souvik Sinha (Fri May 26 2017 - 00:45:37 CDT)
Re: Error regarding missing angles between perturbed groups for fep calculation Vermaas, Joshua (Thu May 25 2017 - 17:29:59 CDT)
RE: Error regarding missing angles between perturbed groups for fep calculation Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Thu May 25 2017 - 16:24:08 CDT)
Re: Error regarding missing angles between perturbed groups for fep calculation Jeff Comer (Thu May 25 2017 - 16:16:18 CDT)
Re: Querries on eABF Jeff Comer (Thu May 25 2017 - 16:06:33 CDT)
RE: performance of NAMD SMP MPI version Bennion, Brian (Thu May 25 2017 - 13:45:13 CDT)
performance of NAMD SMP MPI version jing liang (Thu May 25 2017 - 13:38:10 CDT)
Error regarding missing angles between perturbed groups for fep calculation Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Thu May 25 2017 - 10:49:32 CDT)
Re: Querries on eABF Souvik Sinha (Thu May 25 2017 - 05:02:32 CDT)
RE: pKa calculation with thermodynamic integration (TI) Radak, Brian K (Wed May 24 2017 - 13:29:59 CDT)
Re: pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Wed May 24 2017 - 13:16:46 CDT)
RE: pKa calculation with thermodynamic integration (TI) Radak, Brian K (Wed May 24 2017 - 11:35:50 CDT)
Re: pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Wed May 24 2017 - 10:48:29 CDT)
Re: Equilibrium Energies Brian Radak (Tue May 23 2017 - 15:18:59 CDT)
Equilibrium Energies Theodora Teddy (Tue May 23 2017 - 11:10:19 CDT)
Re: pKa calculation with thermodynamic integration (TI) Brian Radak (Tue May 23 2017 - 09:32:14 CDT)
Re: pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Tue May 23 2017 - 01:04:17 CDT)
Re: colvars to restrain peptide close to lipid Giacomo Fiorin (Sun May 21 2017 - 11:31:42 CDT)
Re: colvars to restrain peptide close to lipid Chitrak Gupta (Sat May 20 2017 - 16:10:35 CDT)
Re: CHARMRUN ERROR Scott Brozell (Fri May 19 2017 - 11:17:18 CDT)
Re: CHARMRUN ERROR Zeki Zeybek (Thu May 18 2017 - 13:38:26 CDT)
Re: CHARMRUN ERROR Scott Brozell (Thu May 18 2017 - 13:28:52 CDT)
Re: CHARMRUN ERROR Zeki Zeybek (Thu May 18 2017 - 02:27:27 CDT)
Re: psfgen readpsf error with no more explanation Vermaas, Joshua (Wed May 17 2017 - 16:12:41 CDT)
psfgen readpsf error with no more explanation Sadegh Faramarzi Ganjabad (Wed May 17 2017 - 15:58:37 CDT)
RE: pKa calculation with thermodynamic integration (TI) Radak, Brian K (Wed May 17 2017 - 09:54:39 CDT)
Re: pKa calculation with thermodynamic integration (TI) Hannes Loeffler (Wed May 17 2017 - 03:37:52 CDT)
Re: pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Wed May 17 2017 - 02:00:11 CDT)
Re: Writing pdb file for a particular frame Sourav Pal (Tue May 16 2017 - 22:18:31 CDT)
Writing pdb file for a particular frame Rabeta Yeasmin (Tue May 16 2017 - 18:18:33 CDT)
Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 Giacomo Fiorin (Tue May 16 2017 - 12:18:18 CDT)
Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 Vlad Cojocaru (Tue May 16 2017 - 10:50:10 CDT)
Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 Giacomo Fiorin (Tue May 16 2017 - 09:39:59 CDT)
Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 Vlad Cojocaru (Tue May 16 2017 - 09:36:38 CDT)
Howto gaussian accelerated MD Francesco Pietra (Tue May 16 2017 - 09:34:11 CDT)
Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 JÃ©rÃ´me HÃ©nin (Tue May 16 2017 - 09:08:46 CDT)
Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 Vlad Cojocaru (Tue May 16 2017 - 08:20:31 CDT)
Re: Pulling protein through membrane without changing the position of membrane Rabeta Yeasmin (Mon May 15 2017 - 13:23:22 CDT)
Re: restraining selected atom's z coordinates Rabeta Yeasmin (Mon May 15 2017 - 13:19:33 CDT)
Re: restraining selected atom's z coordinates Vermaas, Joshua (Mon May 15 2017 - 11:30:55 CDT)
colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 Vlad Cojocaru (Mon May 15 2017 - 04:18:28 CDT)
Re: [NAMD] Outputting PMF at half the time using Metadynamics Giacomo Fiorin (Sun May 14 2017 - 22:20:14 CDT)
[NAMD] Outputting PMF at half the time using Metadynamics The Cromicus Productions (Sun May 14 2017 - 14:04:32 CDT)
Re: restraining selected atom's z coordinates Ajasja LjubetiÄ (Sun May 14 2017 - 01:51:03 CDT)
restraining selected atom's z coordinates Rabeta Yeasmin (Sat May 13 2017 - 19:17:26 CDT)
Re: [NAMD] Problem with colvar "tilt" Giacomo Fiorin (Fri May 12 2017 - 14:00:25 CDT)
Re: [NAMD] Problem with colvar "tilt" Ajasja LjubetiÄ (Fri May 12 2017 - 13:41:54 CDT)
Re: [NAMD] Problem with colvar "tilt" The Cromicus Productions (Fri May 12 2017 - 13:29:17 CDT)
Re: [NAMD] Problem with colvar "tilt" Giacomo Fiorin (Fri May 12 2017 - 08:43:41 CDT)
[NAMD] Problem with colvar "tilt" The Cromicus Productions (Fri May 12 2017 - 08:34:33 CDT)
Re: CHARMRUN ERROR Zeki Zeybek (Fri May 12 2017 - 02:05:13 CDT)
Re: CHARMRUN ERROR Boonstra, S. (Thu May 11 2017 - 15:03:38 CDT)
Re: pKa calculation with thermodynamic integration (TI) Vermaas, Joshua (Thu May 11 2017 - 11:52:48 CDT)
Re: Pulling protein through membrane without changing the position of membrane Amy Rice (Thu May 11 2017 - 12:05:37 CDT)
Pulling protein through membrane without changing the position of membrane Rabeta Yeasmin (Thu May 11 2017 - 11:51:44 CDT)
Re: pKa calculation with thermodynamic integration (TI) Brian Radak (Thu May 11 2017 - 10:27:25 CDT)
CHARMRUN ERROR Zeki Zeybek (Thu May 11 2017 - 02:39:43 CDT)
Re: pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Wed May 10 2017 - 19:36:16 CDT)
RE: MPIRUN SLURM SCRIPT Bennion, Brian (Tue May 09 2017 - 13:07:08 CDT)
RE: energy difference between HSE and HSD Radak, Brian K (Tue May 09 2017 - 11:12:14 CDT)
Re: MPIRUN SLURM SCRIPT Zeki Zeybek (Tue May 09 2017 - 11:00:07 CDT)
Re: MPIRUN SLURM SCRIPT Zeki Zeybek (Tue May 09 2017 - 10:58:29 CDT)
Re: MPIRUN SLURM SCRIPT Vermaas, Joshua (Tue May 09 2017 - 10:48:25 CDT)
RE: energy difference between HSE and HSD Radak, Brian K (Tue May 09 2017 - 10:43:49 CDT)
RE: pKa calculation with thermodynamic integration (TI) Radak, Brian K (Tue May 09 2017 - 10:41:52 CDT)
Re: MPIRUN SLURM SCRIPT Zeki Zeybek (Tue May 09 2017 - 06:02:20 CDT)
Re: MPIRUN SLURM SCRIPT Susmita Ghosh (Tue May 09 2017 - 05:39:23 CDT)
MPIRUN SLURM SCRIPT Zeki Zeybek (Tue May 09 2017 - 05:08:22 CDT)
energy difference between HSE and HSD Hao Dong (Mon May 08 2017 - 23:48:48 CDT)
Re: pKa calculation with thermodynamic integration (TI) Vermaas, Joshua (Mon May 08 2017 - 17:01:05 CDT)
pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Mon May 08 2017 - 14:59:06 CDT)
Question about new NAMD QM/MM code Eric Smoll (Sun May 07 2017 - 22:08:08 CDT)
Re: [NAMD] How to build and simulate a periodic DNA in NAMD The Cromicus Productions (Sun May 07 2017 - 00:03:43 CDT)
Re: [NAMD] How to build and simulate a periodic DNA in NAMD The Cromicus Productions (Sat May 06 2017 - 23:30:26 CDT)
Re: [NAMD] How to build and simulate a periodic DNA in NAMD The Cromicus Productions (Sat May 06 2017 - 19:02:57 CDT)
RE: [NAMD] How to build and simulate a periodic DNA in NAMD Nielsen, Steven (Sat May 06 2017 - 13:49:13 CDT)
[NAMD] How to build and simulate a periodic DNA in NAMD The Cromicus Productions (Sat May 06 2017 - 13:14:34 CDT)
Re: namd 2.12 and plumed 2.3 vlad.cojocaru_at_mpi-muenster.mpg.de (Tue May 02 2017 - 11:50:02 CDT)
Re: namd 2.12 and plumed 2.3 Vlad Cojocaru (Tue May 02 2017 - 10:33:34 CDT)
Re: namd 2.12 and plumed 2.3 yjcoshc_at_gmail.com (Tue May 02 2017 - 11:02:33 CDT)
Re: namd 2.12 and plumed 2.3 Vermaas, Joshua (Tue May 02 2017 - 10:22:01 CDT)
Re: namd 2.12 and plumed 2.3 Giacomo Fiorin (Tue May 02 2017 - 09:45:17 CDT)
Re: namd 2.12 and plumed 2.3 Vlad Cojocaru (Tue May 02 2017 - 09:00:14 CDT)
Re: namd 2.12 and plumed 2.3 Giacomo Fiorin (Tue May 02 2017 - 08:38:06 CDT)
Re: namd 2.12 and plumed 2.3 Vlad Cojocaru (Tue May 02 2017 - 08:12:22 CDT)
Re: Free energy calculation under external bias, (e)ABF/US/etc yjcoshc_at_gmail.com (Tue May 02 2017 - 04:15:21 CDT)
Re: verbs-smp on a single node Jeff Comer (Mon May 01 2017 - 11:22:48 CDT)
Re: Free energy calculation under external bias, (e)ABF/US/etc Giacomo Fiorin (Mon May 01 2017 - 10:10:18 CDT)
Bond-jitter/Total-energy-spikes during energy minimization in vacuum Eric Smoll (Mon May 01 2017 - 02:58:10 CDT)
Free energy calculation under external bias, (e)ABF/US/etc Jim (Fri Apr 28 2017 - 20:25:57 CDT)
Re: compilation of NAMD 2.12 fails David Hardy (Fri Apr 28 2017 - 10:41:18 CDT)
Re: compilation of NAMD 2.12 fails Vlad Cojocaru (Fri Apr 28 2017 - 10:36:12 CDT)
Re: compilation of NAMD 2.12 fails Vlad Cojocaru (Fri Apr 28 2017 - 10:24:18 CDT)
Re: compilation of NAMD 2.12 fails Vlad Cojocaru (Fri Apr 28 2017 - 10:23:24 CDT)
Re: compilation of NAMD 2.12 fails David Hardy (Fri Apr 28 2017 - 10:15:04 CDT)
Re: compilation of NAMD 2.12 fails Vlad Cojocaru (Fri Apr 28 2017 - 09:14:58 CDT)
Re: Custum made residue addition Chitrak Gupta (Fri Apr 28 2017 - 08:11:31 CDT)
Re: More FEP using separated topologies David Huggins (Fri Apr 28 2017 - 03:28:55 CDT)
Re: colvars to restrain peptide close to lipid Giacomo Fiorin (Thu Apr 27 2017 - 15:13:14 CDT)
Re: colvars to restrain peptide close to lipid Chitrak Gupta (Thu Apr 27 2017 - 15:11:17 CDT)
Re: Custum made residue addition Chitrak Gupta (Thu Apr 27 2017 - 14:46:27 CDT)
Re: compilation of NAMD 2.12 fails David Hardy (Thu Apr 27 2017 - 12:36:35 CDT)
Re: compilation of NAMD 2.12 fails Vermaas, Joshua (Thu Apr 27 2017 - 11:37:08 CDT)
compilation of NAMD 2.12 fails Vlad Cojocaru (Thu Apr 27 2017 - 10:02:19 CDT)
Re: Kinetic energy outputs Giacomo Fiorin (Thu Apr 27 2017 - 08:50:37 CDT)
Custum made residue addition Zeki Zeybek (Thu Apr 27 2017 - 08:08:17 CDT)
Equilibration using NPT and Production run using NVE ensemble Akshay Bhatnagar (Thu Apr 27 2017 - 07:47:29 CDT)
Re: Shear flow simulation setup James Starlight (Thu Apr 27 2017 - 07:09:25 CDT)
Kinetic energy outputs matthew reeves (Thu Apr 27 2017 - 06:29:38 CDT)
Re: Can large number of atoms define in colvariables reduce the computational speed in adaptive biased force (ABF) simulation via lowering the GPU utility? sunyeping (Thu Apr 27 2017 - 00:34:49 CDT)
Re: colvars to restrain peptide close to lipid Giacomo Fiorin (Wed Apr 26 2017 - 18:46:50 CDT)
Fwd: colvars to restrain peptide close to lipid Chitrak Gupta (Wed Apr 26 2017 - 17:22:37 CDT)
Re: colvars to restrain peptide close to lipid Jeff Comer (Wed Apr 26 2017 - 15:31:33 CDT)
Re: colvars to restrain peptide close to lipid Chitrak Gupta (Wed Apr 26 2017 - 15:15:10 CDT)
verbs-smp on a single node Jeff Comer (Wed Apr 26 2017 - 15:13:40 CDT)
colvars to restrain peptide close to lipid Chitrak Gupta (Wed Apr 26 2017 - 15:01:23 CDT)
Re: Can large number of atoms define in colvariables reduce the computational speed in adaptive biased force (ABF) simulation via lowering the GPU utility? Giacomo Fiorin (Wed Apr 26 2017 - 13:34:12 CDT)
Can large number of atoms define in colvariables reduce the computational speed in adaptive biased force (ABF) simulation via lowering the GPU utility? sunyeping (Wed Apr 26 2017 - 12:51:17 CDT)
Re: namd 2.12 and plumed 2.3 Giacomo Fiorin (Wed Apr 26 2017 - 12:01:51 CDT)
Re: namd 2.12 and plumed 2.3 Vermaas, Joshua (Wed Apr 26 2017 - 11:43:41 CDT)
Re: namd 2.12 and plumed 2.3 Vlad Cojocaru (Wed Apr 26 2017 - 11:23:54 CDT)
Re: Hybrid QM/MM NAMD: Problem Reading Extended psf files -- But some good news too Angelo Rossi (Wed Apr 26 2017 - 11:00:24 CDT)
Re: namd 2.12 and plumed 2.3 Bassam Haddad (Wed Apr 26 2017 - 10:48:55 CDT)
RE: More FEP using separated topologies Radak, Brian K (Wed Apr 26 2017 - 09:59:47 CDT)
Re: Shear flow simulation setup Giacomo Fiorin (Wed Apr 26 2017 - 09:47:21 CDT)
Re: Hybrid QM/MM NAMD: Problem Reading Extended psf files -- But some good news too Marcelo C. R. Melo (Wed Apr 26 2017 - 09:32:15 CDT)
Shear flow simulation setup James Starlight (Wed Apr 26 2017 - 08:51:54 CDT)
Hybrid QM/MM NAMD: Problem Reading Extended psf files -- But some good news too Angelo Rossi (Wed Apr 26 2017 - 08:06:03 CDT)
Re: Querries on eABF Souvik Sinha (Wed Apr 26 2017 - 06:17:03 CDT)
namd 2.12 and plumed 2.3 Vlad Cojocaru (Wed Apr 26 2017 - 05:20:28 CDT)
Querries on eABF Souvik Sinha (Wed Apr 26 2017 - 01:40:21 CDT)
Re: More FEP using separated topologies David Huggins (Tue Apr 25 2017 - 14:10:06 CDT)
NAMD developer workshop - Chicago, May 22-23, 2017 JoÃ£o Ribeiro (Tue Apr 25 2017 - 07:45:59 CDT)
Re: Segmentation fault during water MD Kevin C Chan (Tue Apr 25 2017 - 06:59:07 CDT)
Continuing SMD from restart files Kevin Chun Chan (Mon Apr 24 2017 - 08:32:18 CDT)
generating topology file Nehir NALINCI (Mon Apr 24 2017 - 07:25:06 CDT)
Klaus Schulten Memorial Issue (http://pubs.acs.org/toc/jpcbfk/121/15) Chris Chipot (Thu Apr 20 2017 - 12:10:34 CDT)
NAMD 2.12 using CUDA 8.0 Wright, David (Thu Apr 20 2017 - 08:40:28 CDT)
RE: Hybrid QM/MM in NAMD 2.12 with Gaussian Stober, Spencer T (Wed Apr 19 2017 - 10:44:18 CDT)
Continuing SMD from restart files Kevin C Chan (Wed Apr 19 2017 - 08:20:03 CDT)
Re: Type of solvent water molecules Boonstra, S. (Wed Apr 19 2017 - 05:20:31 CDT)
Re: Type of solvent water molecules Brian Radak (Tue Apr 18 2017 - 16:56:02 CDT)
Re: Type of solvent water molecules Eduard Schreiner (Tue Apr 18 2017 - 16:21:01 CDT)
Type of solvent water molecules Oscar Bastidas (Tue Apr 18 2017 - 16:05:06 CDT)
Re: What to cite for CHARMM22 Giacomo Fiorin (Tue Apr 18 2017 - 12:42:19 CDT)
What to cite for CHARMM22 Oscar Bastidas (Tue Apr 18 2017 - 12:37:04 CDT)
NAMD developer workshop - Chicago, May 22-23, 2017 JoÃ£o Ribeiro (Tue Apr 18 2017 - 07:45:04 CDT)
Hybrid QM/MM in NAMD 2.12 with Gaussian Stober, Spencer T (Tue Apr 18 2017 - 10:24:03 CDT)
Segmentation fault during water MD nikolaev_at_spbau.ru (Tue Apr 18 2017 - 09:37:10 CDT)
Re: How to calculate 2d surface energy surface on segmented adaptive biased force (ABF) simulations JÃ©rÃ´me HÃ©nin (Tue Apr 18 2017 - 04:47:22 CDT)
Re: How to calculate 2d surface energy surface on segmented adaptive biased force (ABF) simulations sunyeping (Mon Apr 17 2017 - 21:06:19 CDT)
Re: How to calculate 2d surface energy surface on segmented adaptive biased force (ABF) simulations JÃ©rÃ´me HÃ©nin (Mon Apr 17 2017 - 15:22:36 CDT)
Re: how to have large coordinate values in the "coordinates PDB" file Giacomo Fiorin (Mon Apr 17 2017 - 14:05:40 CDT)
Re: how to have large coordinate values in the "coordinates PDB" file Vermaas, Joshua (Mon Apr 17 2017 - 14:03:15 CDT)
how to have large coordinate values in the "coordinates PDB" file Nielsen, Steven (Mon Apr 17 2017 - 13:33:37 CDT)
Re: Slurm Script for Multi Node Run Bennion, Brian (Mon Apr 17 2017 - 11:52:58 CDT)
Re: performance on ~1.5 million atoms system Vermaas, Joshua (Mon Apr 17 2017 - 10:33:04 CDT)
TCBG Live Computational Biophysics Workshop Lectures JoÃ£o Ribeiro (Mon Apr 17 2017 - 09:13:24 CDT)
How to calculate 2d surface energy surface on segmented adaptive biased force (ABF) simulations sunyeping (Mon Apr 17 2017 - 05:54:46 CDT)
performance on ~1.5 million atoms system Steven Neumann (Mon Apr 17 2017 - 00:42:12 CDT)
Slurm Script for Multi Node Run Zeki Zeybek (Sun Apr 16 2017 - 11:42:41 CDT)
generating topology file Nehir NALINCI (Sat Apr 15 2017 - 03:09:07 CDT)
Re: Energy values Vermaas, Joshua (Fri Apr 14 2017 - 17:57:56 CDT)
Energy values matthew reeves (Fri Apr 14 2017 - 16:49:54 CDT)
Best NAMD distribution for COEUS cluster? Bassam Haddad (Thu Apr 13 2017 - 15:27:10 CDT)
Re: Neutralize a box for FEP Grace Brannigan (Wed Apr 12 2017 - 13:08:16 CDT)
RE: Neutralize a box for FEP Radak, Brian K (Wed Apr 12 2017 - 13:17:46 CDT)
Re: Neutralize a box for FEP David Huggins (Wed Apr 12 2017 - 13:05:05 CDT)
RE: Neutralize a box for FEP Radak, Brian K (Wed Apr 12 2017 - 11:14:26 CDT)
Neutralize a box for FEP David Huggins (Wed Apr 12 2017 - 10:30:20 CDT)
Re: Incorporate aluminum oxide monolayer Seibold, Steve Allan (Wed Apr 12 2017 - 09:47:43 CDT)
Incorporate aluminum oxide monolayer The Cromicus Productions (Tue Apr 11 2017 - 14:50:37 CDT)
Re: lipid centering Karteek Bejagam (Tue Apr 11 2017 - 13:26:05 CDT)
Re: lipid centering Vermaas, Joshua (Tue Apr 11 2017 - 13:23:05 CDT)
lipid centering Mihaela Drenscko (Tue Apr 11 2017 - 13:08:24 CDT)
TCBG Live Computational Biophysics Workshop Lectures JoÃ£o Ribeiro (Mon Apr 10 2017 - 08:24:13 CDT)
Re: Standard Output: Benchmark vs Timing Vermaas, Joshua (Sun Apr 09 2017 - 20:58:47 CDT)
Standard Output: Benchmark vs Timing Jim (Fri Apr 07 2017 - 17:31:55 CDT)
charmm parameters for buffer molecules Martin, Erik W (Fri Apr 07 2017 - 15:10:46 CDT)
Post-doc position at ALCF - HPC post-doc in Computational Materials Wei Jiang (Fri Apr 07 2017 - 10:18:55 CDT)
Re: Error : components of colvar "alpha" does not support system force calculation JÃ©rÃ´me HÃ©nin (Fri Apr 07 2017 - 07:06:36 CDT)
Error : components of colvar "alpha" does not support system force calculation Souvik Sinha (Fri Apr 07 2017 - 03:47:11 CDT)
wrong pdb struvture generated while using patch hem_chandra_at_iitg.ernet.in (Fri Apr 07 2017 - 02:06:11 CDT)
Re: psfgen giving wrong structure in the autopdb file Peter Freddolino (Thu Apr 06 2017 - 19:50:01 CDT)
psfgen giving wrong structure in the autopdb file Harish Srinivasan (Thu Apr 06 2017 - 01:37:29 CDT)
FATAL ERROR running apoa1 with NAMD 2.12 Tim.Ho_at_csiro.au (Wed Apr 05 2017 - 01:53:26 CDT)
Re: patch Giacomo Fiorin (Fri Mar 31 2017 - 07:49:16 CDT)
patch hem_chandra_at_iitg.ernet.in (Fri Mar 31 2017 - 04:03:15 CDT)
Re: Fatal Error in NAMD Faramarz Joodaki (Thu Mar 30 2017 - 12:54:13 CDT)
Re: Fatal Error in NAMD Faramarz Joodaki (Thu Mar 30 2017 - 12:24:20 CDT)
Re: Fatal Error in NAMD Giacomo Fiorin (Thu Mar 30 2017 - 12:20:26 CDT)
Fatal Error in NAMD Faramarz Joodaki (Thu Mar 30 2017 - 12:14:51 CDT)
AW: Solvent box fluctuations Götz, Alexander (Wed Mar 29 2017 - 03:37:59 CDT)
patch hem_chandra_at_iitg.ernet.in (Mon Mar 27 2017 - 23:28:53 CDT)
Re: Solvent box fluctuations Vermaas, Joshua (Mon Mar 27 2017 - 12:13:37 CDT)
Solvent box fluctuations GÃ¶tz, Alexander (Mon Mar 27 2017 - 11:56:09 CDT)
Problem in NAMD QMMM Kshatresh Dutta Dubey (Sat Mar 25 2017 - 13:37:25 CDT)
AW: Scaling behaviour of NAMD on hosts with GPU accelerators Norman Geist (Fri Mar 24 2017 - 08:25:52 CDT)
Re: Scaling behaviour of NAMD on hosts with GPU accelrators Boonstra, S. (Fri Mar 24 2017 - 06:41:19 CDT)
Re: AW: Scaling behaviour of NAMD on hosts with GPU accelrators Maxime Boissonneault (Fri Mar 24 2017 - 06:42:04 CDT)
AW: Scaling behaviour of NAMD on hosts with GPU accelrators Norman Geist (Fri Mar 24 2017 - 05:47:39 CDT)
AW: Scaling behaviour of NAMD on hosts with GPU accelrators Norman Geist (Fri Mar 24 2017 - 05:35:00 CDT)
AW: Scaling behaviour of NAMD on hosts with GPU accelrators Norman Geist (Fri Mar 24 2017 - 05:27:46 CDT)
Re: Victor Ovchinnikov (Thu Mar 23 2017 - 16:34:22 CDT)
(no subject) Marco Antonio Ramirez Martinez (Thu Mar 23 2017 - 13:23:33 CDT)
Re: Scaling behaviour of NAMD on hosts with GPU accelrators Jeff Comer (Thu Mar 23 2017 - 12:24:23 CDT)
Scaling behaviour of NAMD on hosts with GPU accelrators Kraus, Sebastian (Thu Mar 23 2017 - 11:18:14 CDT)
Re: Explanation of parameters for NBTABLE's tabulated external file? Wasut Pornpatcharapong (Wed Mar 22 2017 - 16:59:19 CDT)
Re: Explanation of parameters for NBTABLE's tabulated external file? David Hardy (Wed Mar 22 2017 - 14:17:09 CDT)
Re: Explanation of parameters for NBTABLE's tabulated external file? David Hardy (Wed Mar 22 2017 - 14:09:17 CDT)
Re: Explanation of parameters for NBTABLE's tabulated external file? Wasut Pornpatcharapong (Wed Mar 22 2017 - 13:56:15 CDT)
Re: Explanation of parameters for NBTABLE's tabulated external file? Vermaas, Joshua (Wed Mar 22 2017 - 13:09:02 CDT)
Explanation of parameters for NBTABLE's tabulated external file? Wasut Pornpatcharapong (Wed Mar 22 2017 - 12:55:12 CDT)
Hands-On Workshop on Computational Biophysics: May 30 - June 2 in Pittsburgh, PA JoÃ£o Ribeiro KS (Wed Mar 22 2017 - 10:15:40 CDT)
Re: Constraining bonds that aren't hydrogens - splitPatch usefulness ? Jeff Comer (Wed Mar 22 2017 - 08:56:57 CDT)
Constraining bonds that aren't hydrogens - splitPatch usefulness ? Marlon Sidore (Wed Mar 22 2017 - 07:08:50 CDT)
(no subject) Debaditya Mukherjee (Tue Mar 21 2017 - 23:38:56 CDT)
Workshop on MD simulation software design Giacomo Fiorin (Tue Mar 21 2017 - 13:42:55 CDT)
Re: is NVE ensemble for production run justified? Brian Radak (Tue Mar 21 2017 - 09:44:52 CDT)
Re: FATAL ERROR: Duplicate bond PRITI ROY (Tue Mar 21 2017 - 08:25:08 CDT)
is NVE ensemble for production run justified? Akshay Bhatnagar (Tue Mar 21 2017 - 00:13:19 CDT)
Re: Charm++ supports RoCE ? Hyun (Mon Mar 20 2017 - 22:22:40 CDT)
Re: Defining colvars based on a region Giacomo Fiorin (Mon Mar 20 2017 - 20:00:09 CDT)
Defining colvars based on a region Bob Faith (Mon Mar 20 2017 - 19:48:00 CDT)
Re: problem to generate LPS PSF file using PSFGEN ì†¡ì—°í˜¸ (Mon Mar 20 2017 - 19:22:29 CDT)
Problem with namd2 execution on Windows GPU version md_at_novamechanics.com (Fri Mar 17 2017 - 15:57:26 CDT)
Re: problem to generate LPS PSF file using PSFGEN Fotis Baltoumas (Fri Mar 17 2017 - 05:03:42 CDT)
problem to generate LPS PSF file using PSFGEN ì†¡ì—°í˜¸ (Thu Mar 16 2017 - 23:19:36 CDT)
Implicit solvent no non-bonded pairing Eric Pederson (Thu Mar 16 2017 - 19:41:51 CDT)
Charm++ supports RoCE ? Hyun (Thu Mar 16 2017 - 18:06:01 CDT)
generating nodelist and error Hyun (Thu Mar 16 2017 - 10:10:19 CDT)
Re: Some questions about the orthogonality of colvars in ABF. yjcoshc (Wed Mar 15 2017 - 08:39:58 CDT)
Some questions about the orthogonality of colvars in ABF. yjcoshc (Wed Mar 15 2017 - 07:11:46 CDT)
Re: Questions on creating constraints in NAMD Randy J. Zauhar (Sat Mar 11 2017 - 13:01:17 CST)
gbis for acetonitrile hem_chandra_at_iitg.ernet.in (Sat Mar 11 2017 - 00:40:15 CST)
(no subject) Debaditya Mukherjee (Fri Mar 10 2017 - 23:40:50 CST)
RE: Specify number of water molecules:simulation set up in VMD Bennion, Brian (Fri Mar 10 2017 - 13:34:56 CST)
Specify number of water molecules:simulation set up in VMD Rabeta Yeasmin (Fri Mar 10 2017 - 13:21:31 CST)
AW: NAMD-2.12 handful of issues with CUDA Norman Geist (Fri Mar 10 2017 - 05:41:10 CST)
Re: NAMD-2.12 handful of issues with CUDA Ajasja LjubetiÄ (Fri Mar 10 2017 - 05:14:10 CST)
AW: NAMD-2.12 handful of issues with CUDA Norman Geist (Fri Mar 10 2017 - 04:55:47 CST)
NAMD-2.12 handful of issues with CUDA Norman Geist (Fri Mar 10 2017 - 03:16:13 CST)
Re: Cascade MDFF Ryan McGreevy (Thu Mar 09 2017 - 10:53:42 CST)
specify H-bond in CGMD Deng, Jinxia (Nancy) (Thu Mar 09 2017 - 08:42:14 CST)
Re: Cascade MDFF Ryan McGreevy (Thu Mar 09 2017 - 08:25:56 CST)
Cascade MDFF Luba Simhaev (Thu Mar 09 2017 - 02:34:08 CST)
(no subject) Debaditya Mukherjee (Wed Mar 08 2017 - 22:52:17 CST)
Re: TMD: initial and targeted structure does not have same number of atoms Rabeta Yeasmin (Wed Mar 08 2017 - 10:20:26 CST)
Re: Re: problems mutating HID to TYR for free energy calculations Vermaas, Joshua (Wed Mar 08 2017 - 09:45:49 CST)
Re: problems mutating HID to TYR for free energy calculations Nehad Elsalamouny (Tue Mar 07 2017 - 17:39:37 CST)
Re: problems mutating HID to TYR for free energy calculations Brian Radak (Tue Mar 07 2017 - 17:02:27 CST)
Re: problems mutating HID to TYR for free energy calculations Nehad Elsalamouny (Tue Mar 07 2017 - 16:50:32 CST)
Re: TMD: initial and targeted structure does not have same number of atoms Jeff Comer (Tue Mar 07 2017 - 10:15:39 CST)
RE: problems mutating HID to TYR for free energy calculations Radak, Brian K (Tue Mar 07 2017 - 09:49:38 CST)
TMD: initial and targeted structure does not have same number of atoms Rabeta Yeasmin (Tue Mar 07 2017 - 09:42:58 CST)
Choice of bromide ion LJ parameters Harish Srinivasan (Tue Mar 07 2017 - 07:03:16 CST)
problems mutating HID to TYR for free energy calculations Nehad Elsalamouny (Tue Mar 07 2017 - 04:27:28 CST)
Re: AW: REMD on HPC HOUSTON Douglas (Tue Mar 07 2017 - 02:33:29 CST)
Re: Question about applying external force The Cromicus Productions (Mon Mar 06 2017 - 18:27:20 CST)
Re: Question about applying external force Giacomo Fiorin (Mon Mar 06 2017 - 16:23:57 CST)
Re: Question about applying external force The Cromicus Productions (Mon Mar 06 2017 - 15:59:25 CST)
Re: Question about applying external force Giacomo Fiorin (Mon Mar 06 2017 - 15:40:38 CST)
Re: Question about applying external force The Cromicus Productions (Mon Mar 06 2017 - 15:32:36 CST)
Question about applying external force The Cromicus Productions (Mon Mar 06 2017 - 13:56:30 CST)
RE: analyze NAMD trajectory in Curves+ Radak, Brian K (Mon Mar 06 2017 - 12:03:25 CST)
analyze NAMD trajectory in Curves+ Oleksii Zdorevskyi (Mon Mar 06 2017 - 11:46:03 CST)
Carma/grcarma v.1.7 released. Nicholas M Glykos (Mon Mar 06 2017 - 10:31:26 CST)
Re: AW: REMD on HPC Vermaas, Joshua (Mon Mar 06 2017 - 09:47:23 CST)
AW: REMD on HPC Norman Geist (Mon Mar 06 2017 - 09:26:00 CST)
REMD on HPC HOUSTON Douglas (Mon Mar 06 2017 - 08:15:25 CST)
Workshop on Computational Biophysics, Urbana, IL: Application Deadline March 10th JoÃ£o Ribeiro KS (Sat Mar 04 2017 - 15:56:47 CST)
cuda errors when running NAMD sunyeping (Fri Mar 03 2017 - 18:51:34 CST)
AW: vmd-l: Building NAMD 2.12 from Source with IB and CUDA Greipel.Joachim_at_mh-hannover.de (Thu Mar 02 2017 - 05:53:58 CST)
Selecting atoms in NAMD .conf file and time-varying electric field Ben Lowe (Wed Mar 01 2017 - 15:42:55 CST)
Multiple Electric Field simulation Athreya, Nagendra Bala Murali (Wed Mar 01 2017 - 15:13:37 CST)
Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Giacomo Fiorin (Wed Mar 01 2017 - 02:04:00 CST)
Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Bennion, Brian (Mon Feb 27 2017 - 17:36:53 CST)
error during minimization Lara rajam (Mon Feb 27 2017 - 13:07:44 CST)
CPU/GPU energy difference Boonstra, S. (Mon Feb 27 2017 - 05:08:28 CST)
Lipid bilayer and ligand interactions Saleh AlKhalifa (Sun Feb 26 2017 - 08:47:58 CST)
FFTK Determination of Dihedrals to be Scanned Zeki Zeybek (Sun Feb 26 2017 - 08:20:30 CST)
NAMD developer workshop at Chicago IL, May 22-23, 2017 JoÃ£o Ribeiro KS (Fri Feb 24 2017 - 19:23:08 CST)
Re: colvars not scaling well in NAMD 2.10 Chitrak Gupta (Fri Feb 24 2017 - 11:46:32 CST)
Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Bennion, Brian (Fri Feb 24 2017 - 10:33:28 CST)
Re: Hands-On Workshop on Computational Biophysics: April 17-21 in Urbana, IL JoÃ£o Ribeiro KS (Fri Feb 24 2017 - 09:11:34 CST)
Re: colvars not scaling well in NAMD 2.10 Giacomo Fiorin (Thu Feb 23 2017 - 21:58:43 CST)
Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Giacomo Fiorin (Thu Feb 23 2017 - 21:50:08 CST)
colvars not scaling well in NAMD 2.10 Chitrak Gupta (Thu Feb 23 2017 - 17:25:14 CST)
RE: colvars: Error: Feature unavailable:compute total collective force only from one group center Bennion, Brian (Thu Feb 23 2017 - 14:58:54 CST)
RE: colvars: Error: Feature unavailable:compute total collective force only from one group center Bennion, Brian (Thu Feb 23 2017 - 14:35:22 CST)
Re: torsional restrain Lara rajam (Thu Feb 23 2017 - 15:23:31 CST)
Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Giacomo Fiorin (Thu Feb 23 2017 - 14:44:00 CST)
Re: torsional restrain Vermaas, Joshua (Thu Feb 23 2017 - 12:02:18 CST)
Re: torsional restrain Lara rajam (Thu Feb 23 2017 - 11:56:45 CST)
Re: torsional restrain Vermaas, Joshua (Thu Feb 23 2017 - 11:09:02 CST)
Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Bennion, Brian (Thu Feb 23 2017 - 10:38:39 CST)
torsional restrain Lara rajam (Thu Feb 23 2017 - 10:14:21 CST)
Re: MDFF simulations in membrane environment Ryan McGreevy (Thu Feb 23 2017 - 08:33:24 CST)
Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Giacomo Fiorin (Thu Feb 23 2017 - 03:10:20 CST)
Re: Metadynamics state file Giacomo Fiorin (Thu Feb 23 2017 - 03:09:17 CST)
Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Ajasja LjubetiÄ (Thu Feb 23 2017 - 01:36:03 CST)
colvars: Error: Feature unavailable:compute total collective force only from one group center Bennion, Brian (Wed Feb 22 2017 - 18:17:44 CST)
Re: restraints and constraints in NAMD Vermaas, Joshua (Wed Feb 22 2017 - 11:57:14 CST)
Re: MDFF simulations in membrane environment Ryan McGreevy (Wed Feb 22 2017 - 09:28:04 CST)
MDFF simulations in membrane environment Luba Simhaev (Wed Feb 22 2017 - 06:15:09 CST)
restraints and constraints in NAMD Lara rajam (Tue Feb 21 2017 - 17:42:40 CST)
Re: Regarding Error on HB2 Vermaas, Joshua (Tue Feb 21 2017 - 11:28:49 CST)
RE: Questions on creating constraints in NAMD Randy J. Zauhar (Tue Feb 21 2017 - 10:07:18 CST)
Questions on creating constraints in NAMD Randy J. Zauhar (Tue Feb 21 2017 - 09:03:21 CST)
How to define spheres of different sizes and their spatial constrains using NAMD? Sahoo, Dushyant (Tue Feb 21 2017 - 02:40:33 CST)
Regarding Error on HB2 Obayed Ullah (Mon Feb 20 2017 - 18:48:56 CST)
Re: Metadynamics state file Carlo Guardiani (Mon Feb 20 2017 - 13:20:05 CST)
Charm++ Fatal Error Question Oscar Bastidas (Mon Feb 20 2017 - 11:36:53 CST)
Re: pairInteraction commands Brian Radak (Mon Feb 20 2017 - 08:19:54 CST)
pairInteraction commands matthew reeves (Sun Feb 19 2017 - 16:39:27 CST)
Define spheres using NAMD Dushyant Sahoo (Sun Feb 19 2017 - 12:17:37 CST)
mail reg membrane tutorial Vidhya Sankar (Sat Feb 18 2017 - 23:34:54 CST)
Hands-On Workshop on Computational Biophysics: April 17-21 in Urbana, IL JoÃ£o Ribeiro KS (Fri Feb 17 2017 - 16:57:13 CST)
protein stability in a membrane and SMD Martin, Erik W (Fri Feb 17 2017 - 17:14:31 CST)
REST2 patch for NAMD 2.12 Chitrak Gupta (Fri Feb 17 2017 - 14:49:07 CST)
Re: Npt lipid simulation with electrostatics 2 Life Sciences Inc (Fri Feb 17 2017 - 11:04:12 CST)
Re: Metadynamics state file Giacomo Fiorin (Fri Feb 17 2017 - 12:22:05 CST)
Re: Npt lipid simulation with electrostatics 2 Life Sciences Inc (Fri Feb 17 2017 - 10:52:36 CST)
Re: Npt lipid simulation with electrostatics 2 Jeff Comer (Fri Feb 17 2017 - 10:31:43 CST)
RE: Npt lipid simulation with electrostatics 2 Radak, Brian K (Fri Feb 17 2017 - 09:26:20 CST)
Metadynamics state file Carlo Guardiani (Fri Feb 17 2017 - 06:53:31 CST)
Npt lipid simulation with electrostatics 2 Life Sciences Inc (Thu Feb 16 2017 - 16:46:32 CST)
Re: Using 3 GPUs (but not 2) causes energy and temperatures to rise extremely fast in NAMD 2.12 Bryan Roessler (Thu Feb 16 2017 - 12:10:23 CST)
Re: Fixing COM of one atom in selection and letting the other move Vermaas, Joshua (Thu Feb 16 2017 - 10:58:32 CST)
question about Steered Molecular Dynamics Oleksii Zdorevskyi (Wed Feb 15 2017 - 08:38:22 CST)
Re: Fixing COM of one atom in selection and letting the other move Vermaas, Joshua (Tue Feb 14 2017 - 18:12:38 CST)
Fixing COM of one atom in selection and letting the other move Life Sciences Inc (Tue Feb 14 2017 - 12:15:00 CST)
RE: PSFgen failed to guess coordinate due to bad angle CD CG HG2 Radak, Brian K (Fri Feb 10 2017 - 09:36:22 CST)
AW: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE Norman Geist (Fri Feb 10 2017 - 05:34:40 CST)
[NAMD] Obtain dynamical matrix away from equilibrium The Cromicus Productions (Thu Feb 09 2017 - 12:02:35 CST)
Re: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE The Cromicus Productions (Thu Feb 09 2017 - 12:01:55 CST)
RE: PSFgen failed to guess coordinate due to bad angle CD CG HG2 Radak, Brian K (Thu Feb 09 2017 - 10:58:59 CST)
PSFgen failed to guess coordinate due to bad angle CD CG HG2 Sarath Josh M.K (Thu Feb 09 2017 - 03:19:39 CST)
RE: regarding constant velocity steered molecular dynamics Radak, Brian K (Wed Feb 08 2017 - 11:48:09 CST)
Re: PDB file creation Vermaas, Joshua (Wed Feb 08 2017 - 11:37:22 CST)
Re: PDB file creation Chitrak Gupta (Wed Feb 08 2017 - 11:27:29 CST)
Re: PDB file creation Bennion, Brian (Wed Feb 08 2017 - 11:23:57 CST)
Re: PDB file creation matthew reeves (Wed Feb 08 2017 - 11:14:13 CST)
Re: PDB file creation Chitrak Gupta (Wed Feb 08 2017 - 08:46:20 CST)
regarding constant velocity steered molecular dynamics mrinal patel (Wed Feb 08 2017 - 04:07:24 CST)
AW: question about GPU Norman Geist (Wed Feb 08 2017 - 02:24:53 CST)
AW: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE Norman Geist (Wed Feb 08 2017 - 02:22:17 CST)
Using 3 GPUs (but not 2) causes energy and temperatures to rise extremely fast in NAMD 2.12 Bryan Roessler (Tue Feb 07 2017 - 19:55:59 CST)
PDB file creation matthew reeves (Tue Feb 07 2017 - 17:52:08 CST)
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE The Cromicus Productions (Tue Feb 07 2017 - 17:43:40 CST)
Re: Re: How to get ideal alpha-helical, Ï‰-shaped Î³-turn, and turn/310-helix conformations Jessen Lucas (Tue Feb 07 2017 - 10:58:22 CST)
Re: Re: How to get ideal alpha-helical, Ï‰-shaped Î³-turn, and turn/310-helix conformations JÃ©rÃ´me HÃ©nin (Tue Feb 07 2017 - 10:43:53 CST)
Re: How to get ideal alpha-helical, Ï‰-shaped Î³-turn, and turn/310-helix conformations Jessen Lucas (Tue Feb 07 2017 - 09:28:21 CST)
NAMD Acceleration using P100 (GP-GPU) accelerator Atanu Maity (Tue Feb 07 2017 - 03:25:52 CST)
AW: question about GPU Norman Geist (Tue Feb 07 2017 - 03:15:30 CST)
RE: Compiling charm/NAMD with an alternative gcc, e.g. gcc 6.x Radak, Brian K (Mon Feb 06 2017 - 11:27:58 CST)
AW: question about GPU Norman Geist (Mon Feb 06 2017 - 09:47:28 CST)
question about GPU parinaz bashirbanaem (Mon Feb 06 2017 - 09:00:53 CST)
Compiling charm/NAMD with an alternative gcc, e.g. gcc 6.x Greipel.Joachim_at_mh-hannover.de (Mon Feb 06 2017 - 08:54:08 CST)
Re: ++idlepoll Zeki Zeybek (Mon Feb 06 2017 - 02:59:51 CST)
Re: ++idlepoll Francesco Pietra (Mon Feb 06 2017 - 02:37:33 CST)
AW: ++idlepoll Norman Geist (Mon Feb 06 2017 - 02:15:12 CST)
++idlepoll Zeki Zeybek (Mon Feb 06 2017 - 01:21:19 CST)
Re: AW: High pressure calculations faride badalkhani (Sat Feb 04 2017 - 06:11:52 CST)
Re: AW: High pressure calculations Francesco Pietra (Sat Feb 04 2017 - 06:00:53 CST)
Re: AW: High pressure calculations Andrey KALINICHEV (Sat Feb 04 2017 - 05:54:36 CST)
AW: High pressure calculations Norman Geist (Sat Feb 04 2017 - 05:33:49 CST)
Re: Re: Inconsistency between NAMD 2.11 and NAMD 2.12 Bryan Roessler (Fri Feb 03 2017 - 14:47:27 CST)
Re: Re: Inconsistency between NAMD 2.11 and NAMD 2.12 Bryan Roessler (Fri Feb 03 2017 - 14:17:51 CST)
strange diffs in energy output of NAMD 2.9 vs. 2.11 Erik Nordgren (Fri Feb 03 2017 - 14:05:23 CST)
Re: High pressure calculations faride badalkhani (Fri Feb 03 2017 - 13:23:34 CST)
Re: High pressure calculations Vermaas, Joshua (Fri Feb 03 2017 - 11:15:04 CST)
High pressure calculations faride badalkhani (Fri Feb 03 2017 - 10:10:39 CST)
Re: namd2.exe has stopped working, NAMD Energy Richard Overstreet (Thu Feb 02 2017 - 20:46:29 CST)
Re: namd2.exe has stopped working, NAMD Energy Darya Fadavi (Thu Feb 02 2017 - 19:44:09 CST)
Positions for Ph.D. candidates in biomolecular modeling Jan Brezovsky (Thu Feb 02 2017 - 05:30:48 CST)
Re: namd2.exe has stopped working, NAMD Energy Goedde, Chris (Wed Feb 01 2017 - 14:45:02 CST)
Re: about colvar module in NAMD Jessen Lucas (Wed Feb 01 2017 - 13:01:24 CST)
Re: about colvar module in NAMD Jessen Lucas (Wed Feb 01 2017 - 13:00:04 CST)
Re: about colvar module in NAMD Giacomo Fiorin (Wed Feb 01 2017 - 12:49:24 CST)
Re: about colvar module in NAMD Giacomo Fiorin (Wed Feb 01 2017 - 12:34:57 CST)
Re: about colvar module in NAMD Giacomo Fiorin (Wed Feb 01 2017 - 12:31:36 CST)
namd2.exe has stopped working, NAMD Energy Darya Fadavi (Wed Feb 01 2017 - 12:31:15 CST)
about colvar module in NAMD Jessen Lucas (Wed Feb 01 2017 - 11:47:41 CST)
How to calculate the number of solvent molecules for simulations in a specified pressure faride badalkhani (Wed Feb 01 2017 - 04:33:55 CST)
Re: Inconsistency between NAMD 2.11 and NAMD 2.12 Bryan Roessler (Tue Jan 31 2017 - 10:12:07 CST)
Re: Inconsistency between NAMD 2.11 and NAMD 2.12 Bryan Roessler (Tue Jan 31 2017 - 09:47:30 CST)
Inconsistency between NAMD 2.11 and NAMD 2.12 Bryan Roessler (Tue Jan 31 2017 - 00:52:22 CST)
Re: [NAMD] Using as collective variable the minimum of a set of distances Giacomo Fiorin (Mon Jan 30 2017 - 17:07:07 CST)
Re: [NAMD] Using as collective variable the minimum of a set of distances The Cromicus Productions (Mon Jan 30 2017 - 16:53:34 CST)
AW: AW: AW: not a number in NAMD log file Norman Geist (Mon Jan 30 2017 - 01:44:14 CST)
Re: Protein Penetrating Water Box salehesam101 . (Sun Jan 29 2017 - 20:07:08 CST)
Re: Protein Penetrating Water Box Saleh AlKhalifa (Sun Jan 29 2017 - 14:02:05 CST)
Re: [NAMD] Using as collective variable the minimum of a set of distances JÃ©rÃ´me HÃ©nin (Sun Jan 29 2017 - 10:25:38 CST)
Protein Penetrating Water Box Oscar Bastidas (Sun Jan 29 2017 - 03:15:25 CST)
[NAMD] Using as collective variable the minimum of a set of distances The Cromicus Productions (Sat Jan 28 2017 - 17:07:52 CST)
Re: On-the-fly eABF: Problem with the tcl script. Emmanuel MOUTOUSSAMY (Fri Jan 27 2017 - 02:58:38 CST)
Re: On-the-fly eABF: Problem with the tcl script. Chris Chipot (Thu Jan 26 2017 - 07:20:13 CST)
On-the-fly eABF: Problem with the tcl script. Emmanuel MOUTOUSSAMY (Thu Jan 26 2017 - 06:06:52 CST)
Re: basis set for QM-MM dft Francesco Pietra (Thu Jan 26 2017 - 01:19:29 CST)
Re: basis set for QM-MM dft Marcelo C. R. Melo (Wed Jan 25 2017 - 13:18:36 CST)
Re: how do I restart umbrella sampling calculations? Olya Kravchenko (Wed Jan 25 2017 - 09:19:10 CST)
basis set for QM-MM dft Francesco Pietra (Wed Jan 25 2017 - 09:15:43 CST)
Re: how do I restart umbrella sampling calculations? Vermaas, Joshua (Tue Jan 24 2017 - 16:26:39 CST)
Re: how do I restart umbrella sampling calculations? Olya Kravchenko (Tue Jan 24 2017 - 16:11:17 CST)
Re: how do I restart umbrella sampling calculations? Giacomo Fiorin (Tue Jan 24 2017 - 16:09:13 CST)
Re: how do I restart umbrella sampling calculations? Olya Kravchenko (Tue Jan 24 2017 - 15:44:32 CST)
Re: how do I restart umbrella sampling calculations? Giacomo Fiorin (Tue Jan 24 2017 - 15:20:38 CST)
Re: how do I restart umbrella sampling calculations? Olya Kravchenko (Tue Jan 24 2017 - 15:14:55 CST)
Re: how do I restart umbrella sampling calculations? Vermaas, Joshua (Tue Jan 24 2017 - 14:57:36 CST)
Re: how do I restart umbrella sampling calculations? Giacomo Fiorin (Tue Jan 24 2017 - 14:50:41 CST)
how do I restart umbrella sampling calculations? Olya Kravchenko (Tue Jan 24 2017 - 14:39:12 CST)
Re: [NAMD] Using ABF to study separation of two molecules Giacomo Fiorin (Mon Jan 23 2017 - 09:15:16 CST)
Re: [NAMD] Using ABF to study separation of two molecules The Cromicus Productions (Mon Jan 23 2017 - 09:12:39 CST)
Re: [NAMD] Using ABF to study separation of two molecules Giacomo Fiorin (Mon Jan 23 2017 - 08:43:26 CST)
[NAMD] Using ABF to study separation of two molecules The Cromicus Productions (Mon Jan 23 2017 - 01:00:48 CST)
Slurm Run on supercomputer Marisol Oswald (Sun Jan 22 2017 - 18:21:01 CST)
Re: minimizing each structure of a DCD file Giacomo Fiorin (Sun Jan 22 2017 - 11:28:05 CST)
minimizing each structure of a DCD file saeed amini (Sun Jan 22 2017 - 07:21:23 CST)
Re: ABF with alpha colvar? Giacomo Fiorin (Sat Jan 21 2017 - 15:21:21 CST)
ABF with alpha colvar? Douglas Houston (Sat Jan 21 2017 - 11:30:49 CST)
introduction to research on free energies asaffarhi_at_post.tau.ac.il (Fri Jan 20 2017 - 09:34:05 CST)
Re: QM-MM ORCA Charm++ error Could not find QM output file Marcelo C. R. Melo (Fri Jan 20 2017 - 08:33:18 CST)
Re: QM-MM ORCA Charm++ error Could not find QM output file Francesco Pietra (Thu Jan 19 2017 - 11:56:20 CST)
RE: Energy Gradient Plotting Radak, Brian K (Wed Jan 18 2017 - 11:19:04 CST)
Re: AW: not a number in NAMD log file Mohaddeseh Habibzadeh (Wed Jan 18 2017 - 06:44:58 CST)
Energy Gradient Plotting Zeki Zeybek (Wed Jan 18 2017 - 02:19:03 CST)
Re: dihedral colvar Stefano Guglielmo (Wed Jan 18 2017 - 01:43:48 CST)
AW: not a number in NAMD log file Norman Geist (Wed Jan 18 2017 - 01:14:12 CST)
AW: NAMD performance monitor Norman Geist (Wed Jan 18 2017 - 01:10:26 CST)
Drude minimization does not converge Christian Jorgensen (Fri Jan 13 2017 - 10:16:08 CST)
Re: dihedral colvar Giacomo Fiorin (Tue Jan 17 2017 - 20:47:39 CST)
dihedral colvar Stefano Guglielmo (Tue Jan 17 2017 - 19:11:09 CST)
not a number in NAMD log file Mohaddeseh Habibzadeh (Tue Jan 17 2017 - 00:31:55 CST)
Re: QM-MM ORCA Charm++ error Could not find QM output file Marcelo C. R. Melo (Tue Jan 17 2017 - 15:58:58 CST)
Re: Re: Charm++ fatal error with QM-MM MOPAC Marcelo C. R. Melo (Tue Jan 17 2017 - 15:52:04 CST)
Re: QM-MM ORCA Charm++ error Could not find QM output file Francesco Pietra (Tue Jan 17 2017 - 12:10:52 CST)
Re: NAMD performance monitor Vermaas, Joshua (Tue Jan 17 2017 - 10:47:33 CST)
NAMD performance monitor Nikhil Maroli (Tue Jan 17 2017 - 06:42:41 CST)
Re: QM-MM ORCA Charm++ error Could not find QM output file Marcelo C. R. Melo (Mon Jan 16 2017 - 16:17:19 CST)
Re: Re: Charm++ fatal error with QM-MM MOPAC Marcelo C. R. Melo (Mon Jan 16 2017 - 15:52:41 CST)
QM-MM ORCA Charm++ error Could not find QM output file Francesco Pietra (Mon Jan 16 2017 - 01:55:38 CST)
Fwd: Re: Charm++ fatal error with QM-MM MOPAC Francesco Pietra (Sun Jan 15 2017 - 02:53:17 CST)
Re: Re: Charm++ fatal error with QM-MM MOPAC Francesco Pietra (Sun Jan 15 2017 - 01:55:20 CST)
Re: Colvar distance xy to restrain ions Azadeh Alavizargar (Fri Jan 13 2017 - 15:00:16 CST)
Re: Drude minimization does not converge Christian Jorgensen (Fri Jan 13 2017 - 13:21:39 CST)
Re: Calculating gradient of the potential (force field) on each atom. Brian Radak (Fri Jan 13 2017 - 11:34:11 CST)
Re: Drude minimization does not converge Christian Jorgensen (Fri Jan 13 2017 - 11:26:39 CST)
Re: Drude minimization does not converge salehesam_at_gmail.com (Fri Jan 13 2017 - 10:36:41 CST)
Drude minimization does not converge Christian Jorgensen (Fri Jan 13 2017 - 10:19:03 CST)
Re: How to get ideal alpha-helical, Ï‰-shaped Î³-turn, and turn/310-helix conformations JÃ©rÃ´me HÃ©nin (Fri Jan 13 2017 - 02:57:13 CST)
How to get ideal alpha-helical, Ï‰-shaped Î³-turn, and turn/310-helix conformations Jessen Lucas (Thu Jan 12 2017 - 20:09:30 CST)
Calculating gradient of the potential (force field) on each atom. Wasut Pornpatcharapong (Thu Jan 12 2017 - 17:37:55 CST)
Re: Colvar distance xy to restrain ions Olya Kravchenko (Thu Jan 12 2017 - 10:39:00 CST)
Re: Colvar distance xy to restrain ions Azadeh Alavizargar (Thu Jan 12 2017 - 04:30:42 CST)
Colvar distance xy to restrain ions Azadeh Alavizargar (Thu Jan 12 2017 - 02:42:25 CST)
Re: 2.12, cufft problems on a GTX 1070 ? [SOLVED] Nicholas M. Glykos (Wed Jan 11 2017 - 12:51:54 CST)
Re: Solvation free energy difference of alchemical transformation of K+ into Na+ Brian Radak (Wed Jan 11 2017 - 10:20:21 CST)
fatal error in running namd/2.12 sunyeping (Wed Jan 11 2017 - 07:46:01 CST)
Re: Solvation free energy difference of alchemical transformation of K+ into Na+ Abhishek Kumar Singh (Wed Jan 11 2017 - 00:39:11 CST)
Re: multiple replicas metadynamics Giacomo Fiorin (Tue Jan 10 2017 - 15:40:43 CST)
Re: multiple replicas metadynamics Mihaela Drenscko (Tue Jan 10 2017 - 14:57:55 CST)
RE: Solvation free energy difference of alchemical transformation of K+ into Na+ Radak, Brian K (Tue Jan 10 2017 - 14:28:57 CST)
RE: Solvation free energy difference of alchemical transformation of K+ into Na+ Radak, Brian K (Tue Jan 10 2017 - 12:27:07 CST)
Re: multiple replicas metadynamics Giacomo Fiorin (Tue Jan 10 2017 - 11:37:00 CST)
Re: Charm++ fatal error with QM-MM MOPAC Francesco Pietra (Tue Jan 10 2017 - 10:50:58 CST)
Re: Re: Charm++ fatal error with QM-MM MOPAC Francesco Pietra (Tue Jan 10 2017 - 10:40:39 CST)
Re: How to perform REMD of a system a membrane-protein system? Giacomo Fiorin (Tue Jan 10 2017 - 10:09:04 CST)
Re: Solvation free energy difference of alchemical transformation of K+ into Na+ Hannes Loeffler (Tue Jan 10 2017 - 09:59:35 CST)
Re: Solvation free energy difference of alchemical transformation of K+ into Na+ B.W.J. Irwin (Tue Jan 10 2017 - 09:09:52 CST)
Re: Charm++ fatal error with QM-MM MOPAC Marcelo C. R. Melo (Tue Jan 10 2017 - 08:11:02 CST)
Re: Solvation free energy difference of alchemical transformation of K+ into Na+ Hannes Loeffler (Tue Jan 10 2017 - 06:15:02 CST)
Re: multiple replicas metadynamics quo.physics_at_gmail.com (Tue Jan 10 2017 - 05:57:27 CST)
Solvation free energy difference of alchemical transformation of K+ into Na+ Abhishek Kumar Singh (Tue Jan 10 2017 - 05:09:01 CST)
Charm++ fatal error with QM-MM MOPAC Francesco Pietra (Tue Jan 10 2017 - 01:56:35 CST)
Re: multiple replicas metadynamics Ajasja LjubetiÄ (Mon Jan 09 2017 - 23:55:38 CST)
Re: multiple replicas metadynamics Mihaela Drenscko (Mon Jan 09 2017 - 16:20:34 CST)
Re: How to perform REMD of a system a membrane-protein system? Panagiota Kyriakou (Mon Jan 09 2017 - 16:34:03 CST)
Re: multiple replicas metadynamics Mihaela Drenscko (Mon Jan 09 2017 - 16:02:45 CST)
Re: Solvation free energy difference of alchemical transformation of K+ into Na+ Brian Radak (Mon Jan 09 2017 - 10:11:47 CST)
Re: The reason for the formation of bubbles in heating stage Danilo Di Maio (Mon Jan 09 2017 - 09:09:58 CST)
The reason for the formation of bubbles in heating stage Mohaddeseh Habibzadeh (Mon Jan 09 2017 - 08:16:51 CST)
Re: not a number error Mohaddeseh Habibzadeh (Mon Jan 09 2017 - 08:07:12 CST)
Re: not a number error Ajasja LjubetiÄ (Mon Jan 09 2017 - 07:39:15 CST)
not a number error Mohaddeseh Habibzadeh (Mon Jan 09 2017 - 01:53:08 CST)
Re: Solvation free energy difference of alchemical transformation of K+ into Na+ Hannes Loeffler (Mon Jan 09 2017 - 01:55:35 CST)
Re: How to restart metadynamics in namd Giacomo Fiorin (Mon Jan 09 2017 - 00:11:17 CST)
Solvation free energy difference of alchemical transformation of K+ into Na+ Abhishek Kumar Singh (Mon Jan 09 2017 - 00:09:32 CST)
Re: How to restart metadynamics in namd Giacomo Fiorin (Sun Jan 08 2017 - 23:59:54 CST)
How to restart metadynamics in namd Wang, X. Y. (Sun Jan 08 2017 - 22:29:41 CST)
Solvation free energy difference of alchemical transformation of K+ into Na+ Abhishek Kumar Singh (Sun Jan 08 2017 - 22:12:34 CST)
Re: very small cell Brian Radak (Sun Jan 08 2017 - 18:59:15 CST)
Re: multiple replicas metadynamics Giacomo Fiorin (Sun Jan 08 2017 - 17:37:21 CST)
Re: readable output of gbis.coor Harish Srinivasan (Sat Jan 07 2017 - 01:58:23 CST)
readable output of gbis.coor hem_chandra_at_iitg.ernet.in (Sat Jan 07 2017 - 00:43:19 CST)
very small cell å°æ¾¤å‹ (Fri Jan 06 2017 - 20:29:34 CST)
multiple replicas metadynamics Mihaela Drenscko (Fri Jan 06 2017 - 20:24:46 CST)
Re: Regarding: Free energy of alchemical transformation of K + and Na + B.W.J. Irwin (Fri Jan 06 2017 - 08:50:24 CST)
Regarding: Free energy of alchemical transformation of K + and Na + Amit Kumar (Fri Jan 06 2017 - 05:09:35 CST)
Re: Metadynamics simulation Giacomo Fiorin (Thu Jan 05 2017 - 09:51:08 CST)
Constraining bonds that don't include hydrogens Marlon Sidore (Thu Jan 05 2017 - 08:11:06 CST)
Re: Metadynamics simulation Azadeh Alavi (Thu Jan 05 2017 - 06:39:34 CST)
Re: dcd to pdb conversion Srijita Paul (Wed Jan 04 2017 - 13:05:28 CST)
Re: Metadynamics simulation Giacomo Fiorin (Wed Jan 04 2017 - 12:16:25 CST)
RE: dcd to pdb conversion Radak, Brian K (Wed Jan 04 2017 - 10:43:35 CST)
Re: Running IMD with TMD (domain restraints) Giacomo Fiorin (Wed Jan 04 2017 - 08:36:46 CST)
Re: How to perform REMD of a system a membrane-protein system? Giacomo Fiorin (Wed Jan 04 2017 - 08:24:18 CST)
Re: dcd to pdb conversion sonu2kd_at_gmail.com (Wed Jan 04 2017 - 06:26:49 CST)
dcd to pdb conversion Srijita Paul (Wed Jan 04 2017 - 06:18:21 CST)
How to perform REMD of a system a membrane-protein system? Panagiota Kyriakou (Tue Jan 03 2017 - 18:38:54 CST)
(no subject) Raul Araya (Tue Jan 03 2017 - 14:22:09 CST)
Running IMD with TMD (domain restraints) Steven Cohen (Mon Jan 02 2017 - 10:43:09 CST)
Metadynamics simulation Azadeh Alavi (Tue Jan 03 2017 - 09:00:43 CST)
QM-MM flooding potential Francesco Pietra (Tue Jan 03 2017 - 01:40:20 CST)
Fwd: (1) Failure running QM-MM with ORCA and (2) problems preparing input with transition metals Francesco Pietra (Mon Jan 02 2017 - 04:54:19 CST)
Re: The use of NPT or NVT ensemble to observe dynamical parameters Ana Celia Vila Verde (Mon Jan 02 2017 - 04:13:20 CST)
The use of NPT or NVT ensemble to observe dynamical parameters Harish Srinivasan (Mon Jan 02 2017 - 02:27:50 CST)
(1) Failure running QM-MM with ORCA and (2) problems preparing input with transition metals Francesco Pietra (Mon Jan 02 2017 - 01:38:54 CST)
2.12, cufft problems on a GTX 1070 ? Nicholas M Glykos (Sun Jan 01 2017 - 03:56:32 CST)
Linux Ubuntu Workstation Networks: Charmrun> error attaching to node '192.168.1.8': Timeout waiting for node-program to connect Marisol Oswald (Fri Dec 30 2016 - 18:51:28 CST)
Re: Constraint bonds that does not include hydrogrens Karteek Bejagam (Fri Dec 30 2016 - 18:14:17 CST)
Re: MD using implicit solvent Vermaas, Joshua (Fri Dec 30 2016 - 11:03:05 CST)
Re: Re: Re: RMSD based PMF calculation with umbrella sampling Ajasja LjubetiÄ (Fri Dec 30 2016 - 10:46:39 CST)
Re: Re: RMSD based PMF calculation with umbrella sampling Wang, X. Y. (Fri Dec 30 2016 - 06:03:02 CST)
MD using implicit solvent hem_chandra_at_iitg.ernet.in (Fri Dec 30 2016 - 05:51:58 CST)
Fwd: Problems running NAMD QM-MM with ORCA 3.0.3 Francesco Pietra (Fri Dec 30 2016 - 03:51:10 CST)
Problems running NAMD QM-MM with ORCA 3.0.3 Francesco Pietra (Fri Dec 30 2016 - 03:24:04 CST)
Fwd: NAMD 2.12 released Francesco Pietra (Wed Dec 28 2016 - 02:12:14 CST)
Fwd: NAMD 2.12 released Francesco Pietra (Wed Dec 28 2016 - 02:10:55 CST)
Re: Query regarding colvar distanceZ Peter Mawanga (Tue Dec 27 2016 - 20:47:16 CST)
Re: Query regarding colvar distanceZ Vermaas, Joshua (Tue Dec 27 2016 - 19:14:06 CST)
Re: Query regarding colvar distanceZ Peter Mawanga (Tue Dec 27 2016 - 19:07:07 CST)
Re: Query regarding colvar distanceZ Giacomo Fiorin (Tue Dec 27 2016 - 13:20:42 CST)
NAMD parallelisation / patch grid P.-L. Chau (Tue Dec 27 2016 - 04:37:15 CST)
Modifying equilibrium distance for part of carbon nanotubes in parameter file jashnvareh 1395 (Tue Dec 27 2016 - 02:55:42 CST)
Re: NAMD 2.12 released Francesco Pietra (Tue Dec 27 2016 - 01:40:40 CST)
Re: Regarding Trajectory files Harish Srinivasan (Mon Dec 26 2016 - 23:44:52 CST)
Re: Regarding Trajectory files Harish Srinivasan (Mon Dec 26 2016 - 23:44:03 CST)
NAMD 2.12 released Angelo Rossi (Mon Dec 26 2016 - 15:53:42 CST)
Re: Query regarding colvar distanceZ Peter Mawanga (Mon Dec 26 2016 - 11:39:48 CST)
Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file zeynab mohamad hoseyni (Sun Dec 25 2016 - 12:46:28 CST)
Re: Query regarding colvar distanceZ Vermaas, Joshua (Mon Dec 26 2016 - 10:49:38 CST)
Re: Query regarding colvar distanceZ Peter Mawanga (Mon Dec 26 2016 - 09:17:34 CST)
Re: Query regarding colvar distanceZ Peter Mawanga (Mon Dec 26 2016 - 09:07:18 CST)
Re: Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file Abhishek TYAGI (Mon Dec 26 2016 - 08:59:58 CST)
Modifying equilibrium distance for a specific region of carbon nanotube in the parameter file jashnvareh 1395 (Mon Dec 26 2016 - 08:30:59 CST)
Re: Query regarding colvar distanceZ Vermaas, Joshua (Mon Dec 26 2016 - 08:12:23 CST)
Query regarding colvar distanceZ Peter Mawanga (Mon Dec 26 2016 - 06:57:57 CST)
Fwd: Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file zeynab hoseyni (Mon Dec 26 2016 - 06:45:28 CST)
Re: NAMD 2.12 released Francesco Pietra (Mon Dec 26 2016 - 04:17:27 CST)
Regarding Trajectory files Amit Kumar (Sun Dec 25 2016 - 23:18:26 CST)
Fwd: Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file zeynab hoseyni (Sun Dec 25 2016 - 14:31:53 CST)
Modifying the equilibrium distance for a specific region of carbon nanotube in the parameter file zeynab hoseyni (Sun Dec 25 2016 - 12:51:46 CST)
NAMD 2.12 released Jim Phillips (Fri Dec 23 2016 - 12:57:34 CST)
Re: Constraint bonds that does not include hydrogrens Jeff Comer (Thu Dec 22 2016 - 13:24:30 CST)
Re: Constraint bonds that does not include hydrogrens Karteek Bejagam (Thu Dec 22 2016 - 10:00:08 CST)
Re: Constraint bonds that does not include hydrogrens Jeff Comer (Thu Dec 22 2016 - 09:38:50 CST)
RMSD based PMF calculation with umbrella sampling Wang, X. Y. (Thu Dec 22 2016 - 04:26:21 CST)
Constraint bonds that does not include hydrogrens Karteek Bejagam (Wed Dec 21 2016 - 23:00:55 CST)
Re: NAMD_CUDA Jim Phillips (Tue Dec 20 2016 - 23:30:12 CST)
Re: 2.11 how to remove charmrun remote-shell options Jim Phillips (Tue Dec 20 2016 - 23:29:12 CST)
Re: 2.11 how to remove charmrun remote-shell options Scott Brozell (Tue Dec 20 2016 - 19:05:08 CST)
Automate QwikMD set up for a large number of NAMD jobs? Danny Xu (Tue Dec 20 2016 - 15:24:36 CST)
Fw (5): zmhoseyni zmhoseyni (Mon Dec 19 2016 - 13:47:30 CST)
Re: Studying Folding of 870 Small Peptides. Computationally Feasible? Brian Radak (Mon Dec 19 2016 - 09:32:10 CST)
Re: Studying Folding of 870 Small Peptides. Computationally Feasible? Nicholas M. Glykos (Mon Dec 19 2016 - 03:36:15 CST)
Re: Studying Folding of 870 Small Peptides. Computationally Feasible? Peter Freddolino (Sat Dec 17 2016 - 22:04:38 CST)
Re: Studying Folding of 870 Small Peptides. Computationally Feasible? JC Gumbart (Sat Dec 17 2016 - 19:18:46 CST)
Re: Studying Folding of 870 Small Peptides. Computationally Feasible? Eric A Brenner (Sat Dec 17 2016 - 19:02:39 CST)
Re: Studying Folding of 870 Small Peptides. Computationally Feasible? JC Gumbart (Sat Dec 17 2016 - 18:48:50 CST)
Studying Folding of 870 Small Peptides. Computationally Feasible? Eric A Brenner (Sat Dec 17 2016 - 12:35:59 CST)
Re: Writing number of atoms in a specific group to a file Vermaas, Joshua (Fri Dec 16 2016 - 13:12:22 CST)
Re: Writing number of atoms in a specific group to a file Hamed Fadaei (Fri Dec 16 2016 - 12:52:06 CST)
Re: Writing number of atoms in a specific group to a file Brian Radak (Fri Dec 16 2016 - 12:11:04 CST)
Writing number of atoms in a specific group to a file Hamed Fadaei (Fri Dec 16 2016 - 11:35:24 CST)
Re: Problem with using autoPSF on TMCL lipid Giacomo Fiorin (Fri Dec 16 2016 - 11:18:21 CST)
Re: Problem with using autoPSF on TMCL lipid Jeff Comer (Fri Dec 16 2016 - 10:40:17 CST)
Problem with using autoPSF on TMCL lipid salehesam101 . (Fri Dec 16 2016 - 10:11:47 CST)
GBIS intrinsic radii set from aber parm7 Norman Geist (Fri Dec 16 2016 - 02:04:15 CST)
NAMD_CUDA Sana Saeed (Thu Dec 15 2016 - 20:23:18 CST)
Re: psfgen - pdbalias when using readpsf Peter Freddolino (Thu Dec 15 2016 - 15:37:40 CST)
Re: psfgen - pdbalias when using readpsf Vermaas, Joshua (Thu Dec 15 2016 - 15:26:11 CST)
Re: psfgen - pdbalias when using readpsf Peter Freddolino (Thu Dec 15 2016 - 15:03:23 CST)
Re: psfgen - pdbalias when using readpsf Brian Radak (Thu Dec 15 2016 - 14:48:01 CST)
Re: psfgen - pdbalias when using readpsf Peter Freddolino (Thu Dec 15 2016 - 14:40:40 CST)
Re: NVT and NPT simulationd faride badalkhani (Thu Dec 15 2016 - 14:38:24 CST)
psfgen - pdbalias when using readpsf Brian Radak (Thu Dec 15 2016 - 14:28:56 CST)
AW: NVT and NPT simulationd Norman Geist (Thu Dec 15 2016 - 02:20:28 CST)
Re: NAMD Energies Peter Freddolino (Wed Dec 14 2016 - 13:54:52 CST)
Re: NAMD Energies Giacomo Fiorin (Wed Dec 14 2016 - 13:53:02 CST)
RE: NAMD Energies Radak, Brian K (Wed Dec 14 2016 - 13:42:36 CST)
Re: NAMD Energies Giacomo Fiorin (Wed Dec 14 2016 - 13:47:16 CST)
NAMD Energies Chris Goedde (Wed Dec 14 2016 - 13:13:01 CST)
Re: NVT and NPT simulationd faride badalkhani (Wed Dec 14 2016 - 12:14:08 CST)
Re: using colvars to constrain two atoms in a direction Giacomo Fiorin (Wed Dec 14 2016 - 11:11:00 CST)
Re: NVT and NPT simulationd faride badalkhani (Wed Dec 14 2016 - 11:09:40 CST)
Re: using colvars to constrain two atoms in a direction Hamed Fadaei (Wed Dec 14 2016 - 11:02:37 CST)
Re: using colvars to constrain two atoms in a direction Giacomo Fiorin (Wed Dec 14 2016 - 10:49:31 CST)
Re: using colvars to constrain two atoms in a direction Giacomo Fiorin (Wed Dec 14 2016 - 10:40:57 CST)
Re: using colvars to constrain two atoms in a direction Hamed Fadaei (Wed Dec 14 2016 - 10:34:08 CST)
Re: using colvars to constrain two atoms in a direction Giacomo Fiorin (Wed Dec 14 2016 - 10:22:39 CST)
using colvars to constrain two atoms in a direction Hamed Fadaei (Wed Dec 14 2016 - 10:15:20 CST)
AW: NVT and NPT simulationd Norman Geist (Wed Dec 14 2016 - 01:33:16 CST)
NVT and NPT simulationd faride badalkhani (Tue Dec 13 2016 - 23:50:53 CST)
water permeability calculation using NAMD trajectories Pragya Priyadarshini (Tue Dec 13 2016 - 22:39:41 CST)
Re: protonating ASP and GLU Brian Radak (Tue Dec 13 2016 - 13:20:27 CST)
Re: protonating ASP and GLU Giacomo Fiorin (Tue Dec 13 2016 - 13:06:05 CST)
Re: protonating ASP and GLU Nehad Elsalamouny (Tue Dec 13 2016 - 12:48:35 CST)
Re: protonating ASP and GLU Brian Radak (Tue Dec 13 2016 - 08:27:28 CST)
protonating ASP and GLU Nehad Elsalamouny (Tue Dec 13 2016 - 05:58:51 CST)
Re: Setting up symmetry restraints in a homo-dimer with non-equal number of residues Mark Hilge (Mon Dec 12 2016 - 16:55:07 CST)
NAMD_2.12b1 build on Cray XC40 is failing Ianni, James C CTR USARMY RDECOM ARL (US) (Mon Dec 12 2016 - 14:35:32 CST)
RE: FATAL ERROR: Duplicate bond when going from nvt to npt Radak, Brian K (Mon Dec 12 2016 - 09:33:46 CST)
FATAL ERROR: Duplicate bond when going from nvt to npt Marlon Sidore (Mon Dec 12 2016 - 04:02:17 CST)
Re: Problem with alpha colvar in NAMD 2.12b1 JC Gumbart (Fri Dec 09 2016 - 16:58:23 CST)
Re: Problem with alpha colvar in NAMD 2.12b1 Giacomo Fiorin (Fri Dec 09 2016 - 17:14:34 CST)
(no subject) Tom King (Fri Dec 09 2016 - 16:43:07 CST)
Re: Setting up symmetry restraints in a homo-dimer with non-equal number of residues Ryan McGreevy (Fri Dec 09 2016 - 12:46:04 CST)
Re: Setting up symmetry restraints in a homo-dimer with non-equal number of residues Giacomo Fiorin (Fri Dec 09 2016 - 12:34:43 CST)
Setting up symmetry restraints in a homo-dimer with non-equal number of residues Mark Hilge (Fri Dec 09 2016 - 00:17:19 CST)
Re: Problem with alpha colvar in NAMD 2.12b1 Giacomo Fiorin (Thu Dec 08 2016 - 16:04:41 CST)
Problem with alpha colvar in NAMD 2.12b1 Amy Rice (Thu Dec 08 2016 - 15:23:16 CST)
Re: Vermaas, Joshua (Thu Dec 08 2016 - 10:17:25 CST)
Re: Returning energy values from .log file. Ajasja LjubetiÄ (Thu Dec 08 2016 - 02:30:28 CST)
Re: NAMD How to calculate ns/day Abhishek TYAGI (Thu Dec 08 2016 - 01:38:04 CST)
(no subject) Nehir NALINCI (Thu Dec 08 2016 - 01:06:44 CST)
Re: NAMD How to calculate ns/day Shikha Sharma (Wed Dec 07 2016 - 23:01:44 CST)
Re: NAMD How to calculate ns/day Ajasja LjubetiÄ (Wed Dec 07 2016 - 16:59:45 CST)
NAMD How to calculate ns/day Jan Fredin (Wed Dec 07 2016 - 16:02:16 CST)
RE: Returning energy values from .log file. Radak, Brian K (Wed Dec 07 2016 - 15:19:49 CST)
Re: Returning energy values from .log file. Ajasja LjubetiÄ (Wed Dec 07 2016 - 14:41:54 CST)
Re: Returning energy values from .log file. Chitrak Gupta (Wed Dec 07 2016 - 14:36:57 CST)
Returning energy values from .log file. matthew reeves (Wed Dec 07 2016 - 14:16:44 CST)
Re: Minimization error Vermaas, Joshua (Wed Dec 07 2016 - 11:36:44 CST)
Minimization error Santanu Santra (Tue Dec 06 2016 - 23:00:04 CST)
Re: selectively assign HIE or HID for HIS residues Jim Phillips (Tue Dec 06 2016 - 16:08:47 CST)
Re: Low global exclusion count errors! Jim Phillips (Tue Dec 06 2016 - 15:59:34 CST)
Re: AW: NAMD 2.11 on CRAY XK with CPU+GPU Jim Phillips (Tue Dec 06 2016 - 15:54:31 CST)
Re: selectively assign HIE or HID for HIS residues Nehad Elsalamouny (Tue Dec 06 2016 - 15:03:47 CST)
Re: Energy output values Brian Radak (Tue Dec 06 2016 - 13:35:47 CST)
Energy output values matthew reeves (Tue Dec 06 2016 - 13:16:00 CST)
Re: selectively assign HIE or HID for HIS residues Vermaas, Joshua (Tue Dec 06 2016 - 11:03:38 CST)
Re: selectively assign HIE or HID for HIS residues Brian Radak (Mon Dec 05 2016 - 22:13:09 CST)
selectively assign HIE or HID for HIS residues Nehad Elsalamouny (Mon Dec 05 2016 - 20:19:44 CST)
Re: Getting cluster with defined criteria Brian Radak (Sun Dec 04 2016 - 17:54:21 CST)
Getting cluster with defined criteria Peter Mawanga (Sun Dec 04 2016 - 07:05:35 CST)
AW: How to continue RMSD of previous production simulation Norman Geist (Sat Dec 03 2016 - 05:45:35 CST)
AW: How to continue RMSD of previous production simulation Norman Geist (Sat Dec 03 2016 - 05:51:18 CST)
Re: How to continue RMSD of previous production simulation Chitrak Gupta (Fri Dec 02 2016 - 12:43:05 CST)
How to continue RMSD of previous production simulation Farhad Jahanfar (Fri Dec 02 2016 - 12:21:36 CST)
Re: Low global exclusion count error Brian Radak (Fri Dec 02 2016 - 09:25:30 CST)
Re: Low global exclusion count error B.W.J. Irwin (Fri Dec 02 2016 - 04:43:49 CST)
Re: Amber forcefield in namd simulation in parallel version Teerapong Pirojsirikul (Fri Dec 02 2016 - 03:30:11 CST)
AW: Amber forcefield in namd simulation in parallel version Norman Geist (Fri Dec 02 2016 - 01:59:20 CST)
Re: Amber forcefield in namd simulation in parallel version Santanu Santra (Fri Dec 02 2016 - 00:05:35 CST)
Re: Amber forcefield in namd simulation in parallel version Santanu Santra (Thu Dec 01 2016 - 23:00:45 CST)
FATAL ERROR: cuda_check_progress polled 1000000 times over 101.178648 s on step 6418536 sunyeping (Thu Dec 01 2016 - 17:27:36 CST)
Low global exclusion count error faride badalkhani (Thu Dec 01 2016 - 15:21:03 CST)
Spawning too many gpu processes on the first node Robert Sawko (Thu Dec 01 2016 - 13:10:12 CST)
AW: Amber forcefield in namd simulation in parallel version Norman Geist (Thu Dec 01 2016 - 07:58:00 CST)
Amber forcefield in namd simulation in parallel version Santanu Santra (Thu Dec 01 2016 - 06:36:24 CST)
Re: Running gromacs in namd Subbarao Kanchi (Thu Dec 01 2016 - 01:42:24 CST)
AW: Running gromacs in namd Norman Geist (Thu Dec 01 2016 - 01:06:23 CST)
AW: NAMD 2.11 on CRAY XK with CPU+GPU Norman Geist (Thu Dec 01 2016 - 01:04:38 CST)
Re: Running gromacs in namd Subbarao Kanchi (Thu Dec 01 2016 - 00:27:37 CST)
DNA not translocating under electric field Athreya, Nagendra Bala Murali (Wed Nov 30 2016 - 21:20:55 CST)
NAMD 2.11 on CRAY XK with CPU+GPU P.-L. Chau (Wed Nov 30 2016 - 17:47:07 CST)
Re: query on OuputTotalforce Vs OnesiteTotal force ? Bala subramanian (Wed Nov 30 2016 - 07:39:14 CST)
AW: Running gromacs in namd Norman Geist (Wed Nov 30 2016 - 02:45:09 CST)
Re: NVE simulations in NAMD - the right choice of timesteps and parameters Brian Radak (Tue Nov 29 2016 - 12:52:15 CST)
Re: A problem in ABF simulation Karteek Bejagam (Tue Nov 29 2016 - 12:14:44 CST)
Re: NVE simulations in NAMD - the right choice of timesteps and parameters Vlad Cojocaru (Tue Nov 29 2016 - 11:09:40 CST)
Re: query on OuputTotalforce Vs OnesiteTotal force ? Giacomo Fiorin (Tue Nov 29 2016 - 10:20:36 CST)
Re: NVE simulations in NAMD - the right choice of timesteps and parameters Axel Kohlmeyer (Tue Nov 29 2016 - 10:16:11 CST)
Re: query on OuputTotalforce Vs OnesiteTotal force ? Giacomo Fiorin (Tue Nov 29 2016 - 10:14:34 CST)
Re: NVE simulations in NAMD - the right choice of timesteps and parameters Brian Radak (Tue Nov 29 2016 - 10:04:53 CST)
query on OuputTotalforce Vs OnesiteTotal force ? Bala subramanian (Tue Nov 29 2016 - 09:39:39 CST)
How to create 3'-3' phosphodiester linkage for a DNA. Susmita Ghosh (Mon Nov 28 2016 - 23:50:26 CST)
Re: NVE simulations in NAMD - the right choice of timesteps and parameters Felipe Merino (Tue Nov 29 2016 - 07:03:45 CST)
NVE simulations in NAMD - the right choice of timesteps and parameters Harish Srinivasan (Tue Nov 29 2016 - 04:54:32 CST)
Re: Running gromacs in namd Subbarao Kanchi (Tue Nov 29 2016 - 04:25:06 CST)
AW: Running gromacs in namd Norman Geist (Tue Nov 29 2016 - 01:36:48 CST)
Running gromacs in namd Subbarao Kanchi (Tue Nov 29 2016 - 00:30:37 CST)
Re: tclBC during SMD and ABF simulations Olya Kravchenko (Mon Nov 28 2016 - 19:44:01 CST)
tclBC during SMD and ABF simulations Olya Kravchenko (Mon Nov 28 2016 - 12:36:47 CST)
Re: A common tool to read the output of NAMD run Ajasja LjubetiÄ (Mon Nov 28 2016 - 08:34:47 CST)
Re: A common tool to read the output of NAMD run Richard Overstreet (Mon Nov 28 2016 - 08:08:03 CST)
A common tool to read the output of NAMD run Harish Srinivasan (Mon Nov 28 2016 - 06:28:00 CST)
NAMD installation Puneet (Sat Nov 26 2016 - 01:41:14 CST)
Re: Simulation of metalo-binding proteins luca belmonte (Fri Nov 25 2016 - 06:47:10 CST)
Ligand jump out of the protein through NPT ensemle runs mahdi K (Fri Nov 25 2016 - 06:40:31 CST)
Re: Simulation of metalo-binding proteins James Starlight (Thu Nov 24 2016 - 14:44:03 CST)
Re: Simulation of metalo-binding proteins Francesco Pietra (Thu Nov 24 2016 - 14:41:58 CST)
Re: Simulation of metalo-binding proteins James Starlight (Thu Nov 24 2016 - 14:01:08 CST)
Re: REMD Vermaas, Joshua (Thu Nov 24 2016 - 11:07:06 CST)
Low global exclusion count errors! faride badalkhani (Thu Nov 24 2016 - 10:28:53 CST)
AW: Simulation of metalo-binding proteins Daniel MÃ¶ller (Wed Nov 23 2016 - 15:52:53 CST)
REMD kaushik chakraborty (Wed Nov 23 2016 - 13:58:51 CST)
Simulation of metalo-binding proteins James Starlight (Wed Nov 23 2016 - 13:52:38 CST)
Re: Query on colvar distanceZ Giacomo Fiorin (Mon Nov 21 2016 - 11:10:57 CST)
Re: Separate switchdist for electrostatic interactions Fotis Baltoumas (Mon Nov 21 2016 - 09:54:33 CST)
Separate switchdist for electrostatic interactions Peter Mawanga (Mon Nov 21 2016 - 06:17:18 CST)
Re: Charmm++ error Sourav Ray (Sun Nov 20 2016 - 17:12:02 CST)
Re: Charmm++ error Sourav Ray (Sun Nov 20 2016 - 17:10:44 CST)
â€œCannot compile C++ programs with mpicxx" error when compiling charm-6.7 sunyeping (Sun Nov 20 2016 - 13:22:02 CST)
Charmm++ error matthew reeves (Sun Nov 20 2016 - 11:29:25 CST)
Re: Query on colvar distanceZ Karteek Bejagam (Sat Nov 19 2016 - 10:12:36 CST)
Query on colvar distanceZ Bala subramanian (Sat Nov 19 2016 - 08:18:57 CST)
Re: Generate psf file in x-plor format Nehad Elsalamouny (Thu Nov 17 2016 - 19:04:06 CST)
Re: Generate psf file in x-plor format Vermaas, Joshua (Thu Nov 17 2016 - 18:56:55 CST)
Re: Generate psf file in x-plor format Nehad Elsalamouny (Thu Nov 17 2016 - 16:59:53 CST)
Re: Generate psf file in x-plor format Nehad Elsalamouny (Thu Nov 17 2016 - 14:44:40 CST)
Re: Generate psf file in x-plor format Vermaas, Joshua (Thu Nov 17 2016 - 14:56:01 CST)
Pressure Profile. msa5 (Thu Nov 17 2016 - 11:06:48 CST)
Re: Generate psf file in x-plor format Vermaas, Joshua (Thu Nov 17 2016 - 09:47:42 CST)
Generate psf file in x-plor format Nehad Elsalamouny (Thu Nov 17 2016 - 06:07:39 CST)
NAMD GPU+ibverbs on multiple nodes: timeout problems Robert Sawko (Thu Nov 17 2016 - 05:51:21 CST)
Re: K40 benchmark problem in NAMD sonia ziada (Thu Nov 17 2016 - 01:54:59 CST)
K40 benchmark problem in NAMD Atanu Maity (Thu Nov 17 2016 - 01:27:04 CST)
Hands-On Workshop on Integrative Modeling and Simulations Jodi Ann Hadden (Wed Nov 16 2016 - 11:28:03 CST)
Re: Crashes with dihedral PC Giacomo Fiorin (Tue Nov 15 2016 - 22:40:17 CST)
Crashes with dihedral PC Jiyong Park (Tue Nov 15 2016 - 20:28:32 CST)
Re: About pbc Jeff Comer (Tue Nov 15 2016 - 17:40:12 CST)
RE: SMD restraints Allen, Caley R (Tue Nov 15 2016 - 13:30:17 CST)
Re: SMD restraints Giacomo Fiorin (Tue Nov 15 2016 - 13:17:17 CST)
Re: Queries regarding metadynamics and .pmf visualization Giacomo Fiorin (Tue Nov 15 2016 - 10:40:15 CST)
Re: NPT with graphene Jeff Comer (Tue Nov 15 2016 - 08:10:57 CST)
AW: NPT with graphene Norman Geist (Tue Nov 15 2016 - 03:04:09 CST)
Re: Are there features NOT or POORLY supported on GPU ? sonia ziada (Tue Nov 15 2016 - 01:34:34 CST)
Re: SMD restraints Vermaas, Joshua (Mon Nov 14 2016 - 16:26:01 CST)
Re: SMD restraints Giacomo Fiorin (Mon Nov 14 2016 - 15:59:07 CST)
Re: SMD restraints Giacomo Fiorin (Mon Nov 14 2016 - 15:17:59 CST)
SMD restraints Allen, Caley R (Mon Nov 14 2016 - 15:14:09 CST)
Re: NPT with graphene Richard Overstreet (Mon Nov 14 2016 - 15:03:43 CST)
Re: Are there features NOT or POORLY supported on GPU ? Brian Radak (Mon Nov 14 2016 - 14:46:40 CST)
Re: Are there features NOT or POORLY supported on GPU ? Chris Goedde (Mon Nov 14 2016 - 14:30:16 CST)
Re: Are there features NOT or POORLY supported on GPU ? Brian Radak (Mon Nov 14 2016 - 14:24:13 CST)
Re: Need help with TCL script Vermaas, Joshua (Mon Nov 14 2016 - 14:17:08 CST)
Need help with TCL script Nicholus Bhattacharjee (Mon Nov 14 2016 - 13:10:13 CST)
NPT with graphene Richard Overstreet (Mon Nov 14 2016 - 11:29:27 CST)
Are there features NOT or POORLY supported on GPU ? sonia ziada (Mon Nov 14 2016 - 04:11:43 CST)
Re: NAMD2.12b1 and CUDA Jeff Comer (Thu Nov 10 2016 - 17:23:04 CST)
Re: NAMD2.12b1 and CUDA Jim Phillips (Thu Nov 10 2016 - 16:20:31 CST)
Re: NAMD2.12b1 and CUDA Giacomo Fiorin (Thu Nov 10 2016 - 11:09:04 CST)
NAMD2.12b1 and CUDA Jeff Comer (Thu Nov 10 2016 - 09:09:50 CST)
AW: AW: Trigger DCD frame from TCL? Norman Geist (Thu Nov 10 2016 - 02:09:22 CST)
Re: AW: Trigger DCD frame from TCL? Jim Phillips (Wed Nov 09 2016 - 16:48:00 CST)
restraint backbone to keep secondary structure in coarse grain MD Deng, Jinxia (Nancy) (Wed Nov 09 2016 - 10:42:46 CST)
Re: AW: Trigger DCD frame from TCL? Brian Radak (Wed Nov 09 2016 - 07:34:48 CST)
AW: Trigger DCD frame from TCL? Norman Geist (Wed Nov 09 2016 - 02:48:33 CST)
AW: Trigger DCD frame from TCL? Norman Geist (Wed Nov 09 2016 - 02:05:50 CST)
Re: Parameters for determining run time Oscar Bastidas (Tue Nov 08 2016 - 15:33:00 CST)
About pbc Francesco Pietra (Tue Nov 08 2016 - 15:10:56 CST)
Re: Parameters for determining run time Peter Freddolino (Tue Nov 08 2016 - 15:10:04 CST)
Re: Trigger DCD frame from TCL? Brian Radak (Tue Nov 08 2016 - 09:22:24 CST)
Re: Parameters for determining run time Brian Radak (Tue Nov 08 2016 - 09:18:15 CST)
Trigger DCD frame from TCL? Norman Geist (Tue Nov 08 2016 - 09:12:04 CST)
steepest descent Ma'Mon Hatmal (Tue Nov 08 2016 - 08:58:30 CST)
problem in minimization Ma'Mon Hatmal (Tue Nov 08 2016 - 00:01:28 CST)
Re: Parameters for determining run time Vermaas, Joshua (Mon Nov 07 2016 - 18:43:03 CST)
Re: Parameters for determining run time Peter Freddolino (Mon Nov 07 2016 - 21:21:51 CST)
Re: Parameters for determining run time Richard Overstreet (Mon Nov 07 2016 - 19:12:59 CST)
Parameters for determining run time Oscar Bastidas (Mon Nov 07 2016 - 16:10:34 CST)
performance of GPU calculations Hao Dong (Sun Nov 06 2016 - 21:11:40 CST)
Dear NAMD users msa5 (Thu Nov 03 2016 - 17:18:00 CDT)
NAMD 2.12b1 released Jim Phillips (Thu Nov 03 2016 - 17:06:48 CDT)
multiple run commands freeze when using MTS? Brian Radak (Thu Nov 03 2016 - 15:45:40 CDT)
Hi All msa5 (Tue Nov 01 2016 - 22:06:01 CDT)
Re: CHARMM22-STAR force field for NAMD JC Gumbart (Tue Nov 01 2016 - 21:28:04 CDT)
CHARMM22-STAR force field for NAMD Nicholas M. Glykos (Tue Nov 01 2016 - 13:15:48 CDT)
CHARMM22-STAR force field for NAMD Nicholas M. Glykos (Tue Nov 01 2016 - 13:07:39 CDT)
Re: Re: no response from mail list Giacomo Fiorin (Tue Nov 01 2016 - 09:36:49 CDT)
Remembering Klaus Schulten Thomas C. Bishop (Tue Nov 01 2016 - 09:33:31 CDT)
(no subject) Santanu Santra (Mon Oct 31 2016 - 23:22:58 CDT)
Re: no response from mail list Peter Freddolino (Mon Oct 31 2016 - 20:36:12 CDT)
Re: no response from mail list sunyeping (Mon Oct 31 2016 - 20:32:18 CDT)
Re: no response from mail list Oscar Bastidas (Mon Oct 31 2016 - 20:16:50 CDT)
no response from mail list sunyeping (Mon Oct 31 2016 - 19:23:09 CDT)
Re: is it possible to restrict the access of ions to certain volume? Olya Kravchenko (Mon Oct 31 2016 - 15:55:28 CDT)
Re: is it possible to restrict the access of ions to certain volume? Giacomo Fiorin (Mon Oct 31 2016 - 15:43:34 CDT)
is it possible to restrict the access of ions to certain volume? Olya Kravchenko (Mon Oct 31 2016 - 15:28:40 CDT)
Re: NAMD Execution Error Vermaas, Joshua (Mon Oct 31 2016 - 14:09:02 CDT)
Re: Diagnosing CUDA (non)performance Brian Radak (Mon Oct 31 2016 - 13:37:13 CDT)
Diagnosing CUDA (non)performance Chris Goedde (Mon Oct 31 2016 - 07:48:31 CDT)
NAMD Execution Error Oscar Bastidas (Sun Oct 30 2016 - 18:46:19 CDT)
Re: AW: Turning off and back on fixed atoms Brian Radak (Sat Oct 29 2016 - 12:04:57 CDT)
AW: Turning off and back on fixed atoms Norman Geist (Fri Oct 28 2016 - 04:40:22 CDT)
RE: Turning off and back on fixed atoms Radak, Brian K (Thu Oct 27 2016 - 12:05:27 CDT)
AW: vmd-l: Error connecting to localhost on port 3000 and IMD connection ended unexpectedly; connection terminated. Norman Geist (Thu Oct 27 2016 - 07:50:19 CDT)
Re: Problem with minimization Abhishek TYAGI (Thu Oct 27 2016 - 06:13:10 CDT)
Problem with minimization Ma'Mon Hatmal (Thu Oct 27 2016 - 05:22:52 CDT)
Turning off and back on fixed atoms Norman Geist (Thu Oct 27 2016 - 05:14:28 CDT)
NAMD Question: NAMD Message "364"-What does it mean? Oscar Bastidas (Thu Oct 27 2016 - 03:34:17 CDT)
NAMD Question: How to run on 2-chain system Oscar Bastidas (Wed Oct 26 2016 - 20:08:18 CDT)
RE: Switch off rescale temperature after some number of timesteps Radak, Brian K (Wed Oct 26 2016 - 11:12:36 CDT)
Switch off rescale temperature after some number of timesteps Harish Srinivasan (Wed Oct 26 2016 - 01:05:50 CDT)
Re: mail reg compilation of mdenergy Vidhya Sankar (Tue Oct 25 2016 - 20:20:07 CDT)
Re: Using NAMD with NMR structure Pardis Tabaee (Mon Oct 24 2016 - 16:02:48 CDT)
Re: Using NAMD with NMR structure Steve Chou (Mon Oct 24 2016 - 13:18:34 CDT)
fix disulfide bond in coarse grain(CG) model for NAMD Deng, Jinxia (Nancy) (Mon Oct 24 2016 - 11:46:11 CDT)
Re: Using NAMD with NMR structure Pardis Tabaee (Mon Oct 24 2016 - 11:26:09 CDT)
Re: Using NAMD with NMR structure Pardis Tabaee (Mon Oct 24 2016 - 11:20:26 CDT)
Re: Using NAMD with NMR structure Brian Radak (Mon Oct 24 2016 - 09:02:02 CDT)
Re: Using NAMD with NMR structure Pardis Tabaee (Mon Oct 24 2016 - 06:13:04 CDT)
Re: Using NAMD with NMR structure Peter Freddolino (Sun Oct 23 2016 - 05:55:08 CDT)
Using NAMD with NMR structure Oscar Bastidas (Sun Oct 23 2016 - 02:00:14 CDT)
Re: NAMD breaks with wrong timestep GÃ¶tz, Alexander (Sat Oct 22 2016 - 10:19:42 CDT)
Re: NAMD breaks with wrong timestep Brian Radak (Fri Oct 21 2016 - 15:20:19 CDT)
Re: Minimization failing on one machine only David Hardy (Fri Oct 21 2016 - 15:16:47 CDT)
Re: Minimization failing on one machine only Chris Goedde (Fri Oct 21 2016 - 14:11:42 CDT)
Re: NAMD breaks with wrong timestep Axel Kohlmeyer (Fri Oct 21 2016 - 10:54:00 CDT)
Re: NAMD breaks with wrong timestep Vermaas, Joshua (Fri Oct 21 2016 - 10:49:22 CDT)
Re: NAMD breaks with wrong timestep Brian Radak (Fri Oct 21 2016 - 10:41:46 CDT)
NAMD breaks with wrong timestep Götz, Alexander (Fri Oct 21 2016 - 08:23:33 CDT)
Re: mail reg compilation of mdenergy Axel Kohlmeyer (Wed Oct 19 2016 - 14:27:04 CDT)
Re: mail reg compilation of mdenergy David Hardy (Wed Oct 19 2016 - 14:11:32 CDT)
Re: fix disulfide bridge in coarse grain MD Fotis Baltoumas (Wed Oct 19 2016 - 12:36:11 CDT)
mail reg compilation of mdenergy Vidhya Sankar (Wed Oct 19 2016 - 12:08:12 CDT)
fix disulfide bridge in coarse grain MD Deng, Jinxia (Nancy) (Wed Oct 19 2016 - 11:54:59 CDT)
Re: Minimization failing on one machine only Ajasja LjubetiÄ (Sat Oct 15 2016 - 01:50:29 CDT)
Minimization failing on one machine only Chris Goedde (Fri Oct 14 2016 - 15:34:10 CDT)
Re: Collecting average energies via Tcl callback? Subbarao Kanchi (Thu Oct 13 2016 - 19:20:39 CDT)
Collecting average energies via Tcl callback? Brian Radak (Thu Oct 13 2016 - 11:19:40 CDT)
AW: Re: AW: Reason: FATAL ERROR: Unknown command-line option ++local Norman Geist (Tue Oct 11 2016 - 00:33:25 CDT)
Re: AW: Reason: FATAL ERROR: Unknown command-line option ++local sunyeping (Mon Oct 10 2016 - 21:55:27 CDT)
RE: visualizing and analyzing long simulation Deng, Jinxia (Nancy) (Mon Oct 10 2016 - 10:51:42 CDT)
Re: visualizing and analyzing long simulation Richard Overstreet (Mon Oct 10 2016 - 11:48:28 CDT)
visualizing and analyzing long simulation Dhiraj Srivastava (Mon Oct 10 2016 - 10:41:53 CDT)
AW: NAMD running on a Cluster of Ubuntu Linux Norman Geist (Mon Oct 10 2016 - 01:27:59 CDT)
AW: Reason: FATAL ERROR: Unknown command-line option ++local Norman Geist (Mon Oct 10 2016 - 01:24:44 CDT)
NAMD running on a Cluster of Ubuntu Linux Marisol Oswald (Sun Oct 09 2016 - 18:37:55 CDT)
Reason: FATAL ERROR: Unknown command-line option ++local å™ä¸šå¹³ (Sun Oct 09 2016 - 14:09:47 CDT)
Re: question regarding rmsd dhirajks_at_gmail.com (Thu Oct 06 2016 - 17:37:23 CDT)
Re: question regarding rmsd Leandro MartÃnez (Wed Oct 05 2016 - 15:58:39 CDT)
RE: question regarding rmsd Radak, Brian K (Wed Oct 05 2016 - 15:39:01 CDT)
Re: question regarding rmsd Dhiraj Srivastava (Wed Oct 05 2016 - 14:02:32 CDT)
Re: question regarding rmsd Pardis Tabaee (Wed Oct 05 2016 - 13:34:41 CDT)
RE: question regarding rmsd Radak, Brian K (Wed Oct 05 2016 - 11:18:12 CDT)
Re: question regarding rmsd Roshan Shrestha (Wed Oct 05 2016 - 11:07:09 CDT)
Re: question regarding rmsd dhirajks_at_gmail.com (Wed Oct 05 2016 - 11:03:41 CDT)
Re: Tcl clock Giacomo Fiorin (Wed Oct 05 2016 - 10:58:47 CDT)
Re: question regarding rmsd Pardis Tabaee (Wed Oct 05 2016 - 10:55:01 CDT)
Re: Tcl clock Laura Joana (Wed Oct 05 2016 - 10:42:00 CDT)
Re: Tcl clock Mayne, Christopher G (Wed Oct 05 2016 - 09:51:15 CDT)
question regarding rmsd Dhiraj Srivastava (Tue Oct 04 2016 - 16:07:43 CDT)
Tcl clock Laura Joana (Tue Oct 04 2016 - 14:10:12 CDT)
Re: Switch function equation Brian Radak (Mon Oct 03 2016 - 21:16:58 CDT)
(no subject) Sourav Pal (Mon Oct 03 2016 - 02:44:00 CDT)
Switch function equation Faramarz Joodaki (Sun Oct 02 2016 - 23:57:40 CDT)
stripping off water from DCD file except structural water Dhiraj Srivastava (Sun Oct 02 2016 - 22:57:24 CDT)
Re: Oxidized cysteine parameters for CHARMM36 Brian Radak (Fri Sep 30 2016 - 09:35:08 CDT)
Oxidized cysteine parameters for CHARMM36 Gergely Gyimesi (Fri Sep 30 2016 - 08:40:04 CDT)
Re: Half of the structure goes out of the simulation box! Ana Celia Vila Verde (Fri Sep 30 2016 - 07:31:03 CDT)
Re: Half of the structure goes out of the simulation box! Richard Overstreet (Fri Sep 30 2016 - 06:25:19 CDT)
Half of the structure goes out of the simulation box! faride badalkhani (Fri Sep 30 2016 - 05:18:51 CDT)
dcd file frame number Dhiraj Srivastava (Thu Sep 29 2016 - 22:22:54 CDT)
Hands-On Workshop on Computational Biophysics: November 14-18 in Atlanta, GA Jodi Ann Hadden (Thu Sep 29 2016 - 00:27:31 CDT)
ACS COMP Division awards deadline this week Carlos Simmerling (Wed Sep 28 2016 - 11:34:52 CDT)
Shrinking a polymer to match its density using pbc Sonu Kumar (Wed Sep 28 2016 - 10:21:11 CDT)
RE: Martini CG models parameters errors Mahad Gatti (Wed Sep 28 2016 - 05:40:51 CDT)
RE: Wrapall on or off? Radak, Brian K (Tue Sep 27 2016 - 10:50:33 CDT)
Wrapall on or off? sunyeping (Tue Sep 27 2016 - 00:14:49 CDT)
Re: graphene with proteins Zeina Salman (Mon Sep 26 2016 - 16:02:36 CDT)
Re: graphene with proteins Jeff Comer (Mon Sep 26 2016 - 15:18:07 CDT)
Re: Martini CG models parameters errors Fotis Baltoumas (Mon Sep 26 2016 - 14:58:52 CDT)
Re: Martini CG models parameters errors Vermaas, Joshua (Mon Sep 26 2016 - 10:48:56 CDT)
RE: Martini CG models parameters errors Mahad Gatti (Mon Sep 26 2016 - 04:01:32 CDT)
graphene with proteins Zeina Salman (Sun Sep 25 2016 - 19:42:51 CDT)
FEP double annihilation Carlo Guardiani (Fri Sep 23 2016 - 13:28:30 CDT)
Re: Coordinate DCD file was not created during restart of adaptive biasing force simulation using colvars. JÃ©rÃ´me HÃ©nin (Thu Sep 22 2016 - 14:34:27 CDT)
Re: Martini CG models parameters errors Vermaas, Joshua (Thu Sep 22 2016 - 10:36:40 CDT)
Martini CG models parameters errors Mahad Gatti (Thu Sep 22 2016 - 10:07:34 CDT)
NAMD Equil Config Jackson Cavett (Thu Sep 22 2016 - 07:24:53 CDT)
Re: Coordinate DCD file was not created during restart of adaptive biasing force simulation using colvars. JÃ©rÃ´me HÃ©nin (Thu Sep 22 2016 - 05:04:25 CDT)
Coordinate DCD file was not created during restart of adaptive biasing force simulation using colvars. Zach Bonham (Wed Sep 21 2016 - 15:15:45 CDT)
Re: Running REMD Nicolas Martin (Wed Sep 21 2016 - 03:26:18 CDT)
Re: Running REMD Giacomo Fiorin (Mon Sep 19 2016 - 11:22:52 CDT)
Hands-On Workshop on Computational Biophysics: October 17-21 in Urbana, IL Jodi Ann Hadden (Fri Sep 16 2016 - 15:35:45 CDT)
COORDINATE DCD FILE WAS NOT CREATED Mihaela Drenscko (Thu Sep 15 2016 - 15:42:20 CDT)
AW: NAMD2.11 DCD HEADER PROBLEM Norman Geist (Thu Sep 15 2016 - 01:09:39 CDT)
Re: Umbrella sampling colvars DistanceZ deviates a lot Giacomo Fiorin (Wed Sep 14 2016 - 08:32:43 CDT)
Re: NAMD2.11 DCD HEADER PROBLEM Marco Sant (Wed Sep 14 2016 - 06:37:02 CDT)
Re: NAMD2.11 DCD HEADER PROBLEM Sourav Ray (Wed Sep 14 2016 - 06:10:20 CDT)
NAMD2.11 DCD HEADER PROBLEM Marco Sant (Wed Sep 14 2016 - 05:35:31 CDT)
Running REMD Nicolas Martin (Wed Sep 14 2016 - 03:10:55 CDT)
GPU acceleration using K40 and k80 Atanu Maity (Wed Sep 14 2016 - 00:32:00 CDT)
Re: Umbrella sampling colvars DistanceZ deviates a lot Kevin C Chan (Tue Sep 13 2016 - 23:10:21 CDT)
Re: Gradual Heating Periodic Error Jackson Cavett (Tue Sep 13 2016 - 15:39:42 CDT)
Re: Umbrella sampling colvars DistanceZ deviates a lot Sourav Ray (Tue Sep 13 2016 - 15:22:47 CDT)
Re: Umbrella sampling colvars DistanceZ deviates a lot Giacomo Fiorin (Tue Sep 13 2016 - 15:16:14 CDT)
Re: Gradual Heating Periodic Error Hardy, David Joseph (Tue Sep 13 2016 - 14:13:52 CDT)
Re: Umbrella sampling colvars DistanceZ deviates a lot Tabris Chun Chan (Tue Sep 13 2016 - 12:27:25 CDT)
Re: Gradual Heating Periodic Error david gae (Tue Sep 13 2016 - 12:03:07 CDT)
Re: Umbrella sampling colvars DistanceZ deviates a lot Giacomo Fiorin (Tue Sep 13 2016 - 11:23:56 CDT)
Umbrella sampling colvars DistanceZ deviates a lot Kevin C Chan (Tue Sep 13 2016 - 11:19:08 CDT)
Re: REMD and sortreplicas program Horia Jalily Hasani (Tue Sep 13 2016 - 10:34:22 CDT)
Re: Gradual Heating Periodic Error Jackson Cavett (Tue Sep 13 2016 - 10:32:22 CDT)
Re: Gradual Heating Periodic Error david gae (Tue Sep 13 2016 - 09:27:25 CDT)
Re: Gradual Heating Periodic Error Ajasja LjubetiÄ (Tue Sep 13 2016 - 09:15:38 CDT)
Re: Gradual Heating Periodic Error Jackson Cavett (Tue Sep 13 2016 - 09:01:43 CDT)
Gradual Heating Periodic Error Jackson Cavett (Tue Sep 13 2016 - 08:34:30 CDT)
AW: REMD and sortreplicas program Norman Geist (Tue Sep 13 2016 - 01:19:34 CDT)
Re: PMF decompostion Azadeh Alavi (Mon Sep 12 2016 - 13:34:22 CDT)
RE: PMF decompostion Radak, Brian K (Mon Sep 12 2016 - 12:31:48 CDT)
Re: REMD and sortreplicas program Horia Jalily Hasani (Mon Sep 12 2016 - 11:21:55 CDT)
PMF decompostion Azadeh Alavi (Mon Sep 12 2016 - 06:49:50 CDT)
AW: REMD and sortreplicas program Norman Geist (Mon Sep 12 2016 - 01:38:01 CDT)
AW: REMD and sortreplicas program Norman Geist (Mon Sep 12 2016 - 01:05:39 CDT)
Shear Stress modelling in NAMD James Starlight (Sun Sep 11 2016 - 05:12:26 CDT)
Re: Simulated annealing, in solvent or in vacuum? Roshan Shrestha (Fri Sep 09 2016 - 03:17:37 CDT)
RE: convert .xyz file in .psf file for non-protein molecule grenier_at_cinam.univ-mrs.fr (Fri Sep 09 2016 - 02:51:25 CDT)
Simulated annealing, in solvent or in vacuum? faride badalkhani (Thu Sep 08 2016 - 14:21:26 CDT)
RE: convert .xyz file in .psf file for non-protein molecule Radak, Brian K (Thu Sep 08 2016 - 12:39:04 CDT)
Re: REMD and sortreplicas program Horia Jalily Hasani (Thu Sep 08 2016 - 12:22:39 CDT)
RE: Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 11:22:31 CDT)
Re: Query regarding parameter file generation of non standard residue Vermaas, Joshua (Thu Sep 08 2016 - 11:19:05 CDT)
RE: Query regarding parameter file generation of non standard residue Bennion, Brian (Thu Sep 08 2016 - 11:07:13 CDT)
Re: Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 11:01:22 CDT)
Re: convert .xyz file in .psf file for non-protein molecule Axel Kohlmeyer (Thu Sep 08 2016 - 10:41:07 CDT)
convert .xyz file in .psf file for non-protein molecule grenier_at_cinam.univ-mrs.fr (Thu Sep 08 2016 - 10:20:03 CDT)
query in the equilibration step d.ronika_at_iitg.ernet.in (Thu Sep 08 2016 - 07:32:32 CDT)
Re: Query regarding parameter file generation of non standard residue Abhishek TYAGI (Thu Sep 08 2016 - 06:37:37 CDT)
Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 04:54:35 CDT)
Re: Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 02:36:31 CDT)
AW: REMD and sortreplicas program Norman Geist (Thu Sep 08 2016 - 01:41:21 CDT)
Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 00:12:37 CDT)
REMD and sortreplicas program Horia Jalily Hasani (Wed Sep 07 2016 - 19:10:49 CDT)
Hands-On Workshop on Computational Biophysics: October 17-21 in Urbana, IL Jodi Ann Hadden (Wed Sep 07 2016 - 18:06:53 CDT)
Re: Query regarding parameter file generation of a non standard residue Vermaas, Joshua (Wed Sep 07 2016 - 16:49:15 CDT)
Query regarding parameter file generation of a non standard residue Mahrukh Imtiaz (Wed Sep 07 2016 - 15:12:14 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Wed Sep 07 2016 - 09:17:03 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Wed Sep 07 2016 - 01:14:08 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Tue Sep 06 2016 - 16:43:30 CDT)
The needed time for a MD simulation faride badalkhani (Mon Sep 05 2016 - 10:11:08 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Mon Sep 05 2016 - 06:03:13 CDT)
ION CHANNEL gating mechanism Shambo Hore (Sat Sep 03 2016 - 05:42:46 CDT)
PDB File of Primary structure and Simulation Emerson Macedo (Fri Sep 02 2016 - 11:19:18 CDT)
Re: ion escapes the channel during US simulation Vermaas, Joshua (Thu Sep 01 2016 - 10:27:16 CDT)
Re: ion escapes the channel during US simulation Olya Kravchenko (Thu Sep 01 2016 - 10:17:08 CDT)
Re: ion escapes the channel during US simulation Vermaas, Joshua (Thu Sep 01 2016 - 09:44:22 CDT)
did anyone built NAMD with PLUMED on XSEDE Maksym Korablyov (Thu Sep 01 2016 - 09:36:07 CDT)
Re: ion escapes the channel during US simulation Olya Kravchenko (Thu Sep 01 2016 - 09:03:14 CDT)
Re: NAMD Question: Generating ensemble of structures Brian Radak (Thu Sep 01 2016 - 08:44:10 CDT)
AW: FATAL ERROR CUDA error during equilibration using NAMD Norman Geist (Thu Sep 01 2016 - 01:15:55 CDT)
FATAL ERROR CUDA error during equilibration using NAMD Abraham A. Gutierrez Hernandez (Tue Aug 30 2016 - 18:27:38 CDT)
Re: ion escapes the channel during US simulation Amy Rice (Wed Aug 31 2016 - 10:40:16 CDT)
AW: NAMD Question: Generating ensemble of structures Norman Geist (Wed Aug 31 2016 - 01:29:49 CDT)
NAMD Question: Generating ensemble of structures Oscar Bastidas (Wed Aug 31 2016 - 00:52:20 CDT)
Topology and parameter files for liquid methane Monika Madhavi (Wed Aug 31 2016 - 00:24:24 CDT)
ion escapes the channel during US simulation Olya Kravchenko (Tue Aug 30 2016 - 16:17:26 CDT)
(no subject) krishna (Mon Aug 29 2016 - 03:03:21 CDT)
Re: targetCenters in Umbrella Sampling Vermaas, Joshua (Wed Aug 24 2016 - 18:04:31 CDT)
targetCenters in Umbrella Sampling Olya Kravchenko (Wed Aug 24 2016 - 17:50:36 CDT)
Re: PMF calculation input files Olya Kravchenko (Wed Aug 24 2016 - 16:23:30 CDT)
Re: interpretation of eigenvec colvar? JC Gumbart (Tue Aug 23 2016 - 22:12:48 CDT)
Re: interpretation of eigenvec colvar? Giacomo Fiorin (Tue Aug 23 2016 - 20:29:37 CDT)
interpretation of eigenvec colvar? JC Gumbart (Tue Aug 23 2016 - 20:02:37 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Tue Aug 23 2016 - 14:28:36 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Tue Aug 23 2016 - 14:16:28 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Tue Aug 23 2016 - 13:59:31 CDT)
Re: NAMD equilibrium step Brian Radak (Tue Aug 23 2016 - 13:55:47 CDT)
Re: PMF calculation input files Vermaas, Joshua (Tue Aug 23 2016 - 11:02:01 CDT)
Re: PMF calculation input files Olya Kravchenko (Tue Aug 23 2016 - 10:01:05 CDT)
Re: PMF calculation input files Vermaas, Joshua (Mon Aug 22 2016 - 16:27:34 CDT)
Shrinking a molecule (Colvars and Constant Pressure not working) Sonu Kumar (Mon Aug 22 2016 - 15:21:48 CDT)
Re: PMF calculation input files Olya Kravchenko (Mon Aug 22 2016 - 15:10:57 CDT)
Re: PMF calculation input files Vermaas, Joshua (Mon Aug 22 2016 - 11:23:58 CDT)
PMF calculation input files Olya Kravchenko (Mon Aug 22 2016 - 10:30:28 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Mon Aug 22 2016 - 07:34:17 CDT)
NAMD equilibrium step d.ronika_at_iitg.ernet.in (Mon Aug 22 2016 - 00:34:01 CDT)
Re: Graphene Oxide Parameter File Jeff Comer (Sat Aug 20 2016 - 16:25:07 CDT)
Graphene Oxide Parameter File Marisol Oswald (Sat Aug 20 2016 - 14:25:38 CDT)
Re: how to rerun a namd trajectory in order to complement the missing snapshots? Brian Radak (Fri Aug 19 2016 - 07:54:54 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Fri Aug 19 2016 - 04:00:59 CDT)
RE: Autocorrelation function of Rg goes down without fluctuation around zero Lennart Nilsson (Fri Aug 19 2016 - 01:42:03 CDT)
how to rerun a namd trajectory in order to complement the missing snapshots? sunyeping (Thu Aug 18 2016 - 22:35:51 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 13:50:23 CDT)
RE: Autocorrelation function of Rg goes down without fluctuation around zero Lennart Nilsson (Thu Aug 18 2016 - 13:29:40 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Thu Aug 18 2016 - 11:37:31 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 11:31:05 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 11:27:39 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Thu Aug 18 2016 - 11:20:22 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 11:16:57 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Thu Aug 18 2016 - 11:00:16 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 10:31:53 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Thu Aug 18 2016 - 10:21:30 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 10:16:34 CDT)
Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Thu Aug 18 2016 - 09:47:02 CDT)
Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 04:21:07 CDT)
Re: AW: Energy minimization Vermaas, Joshua (Wed Aug 17 2016 - 10:55:14 CDT)
Re: AW: Energy minimization d.ronika_at_iitg.ernet.in (Wed Aug 17 2016 - 05:09:01 CDT)
AW: Energy minimization Norman Geist (Tue Aug 16 2016 - 23:53:20 CDT)
Hands-On Workshop on Computational Biophysics: November 14-18 in Atlanta, GA Jodi Ann Hadden (Tue Aug 16 2016 - 15:41:22 CDT)
Hands-On Workshop on Computational Biophysics: October 17-21 in Urbana, IL Jodi Ann Hadden (Tue Aug 16 2016 - 15:21:32 CDT)
Re: Lipid Bilayer Shearing Vermaas, Joshua (Tue Aug 16 2016 - 13:06:52 CDT)
Re: Lipid Bilayer Shearing Sachin Natesh (Tue Aug 16 2016 - 13:01:45 CDT)
Re: Lipid Bilayer Shearing Vermaas, Joshua (Tue Aug 16 2016 - 12:25:06 CDT)
Lipid Bilayer Shearing Sachin Natesh (Tue Aug 16 2016 - 12:01:15 CDT)
Introducing PDBManip Ali Khanlarkhani (Tue Aug 16 2016 - 10:10:05 CDT)
Re: Energy minimization Aron Broom (Tue Aug 16 2016 - 09:57:04 CDT)
Energy minimization d.ronika_at_iitg.ernet.in (Mon Aug 15 2016 - 00:05:12 CDT)
Re: PMF Calculation Brian Radak (Sun Aug 14 2016 - 16:36:06 CDT)
Re: psfgen: creating segments without extra hydrogens? Brian Radak (Sun Aug 14 2016 - 16:39:59 CDT)
psfgen: creating segments without extra hydrogens? Emerson Macedo (Sat Aug 13 2016 - 13:58:49 CDT)
PMF Calculation Crystal Liu (Fri Aug 12 2016 - 19:15:46 CDT)
RE: Is it possible to perform NVT FEP on a fluid system? Radak, Brian K (Tue Aug 09 2016 - 10:22:59 CDT)
RE: Is it possible to perform NVT FEP on a fluid system? Jeffrey Potoff (Tue Aug 09 2016 - 12:10:10 CDT)
RE: Is it possible to perform NVT FEP on a fluid system? Radak, Brian K (Tue Aug 09 2016 - 11:51:05 CDT)
Re: Energy minimization in NAMD Ajasja LjubetiÄ (Tue Aug 09 2016 - 11:27:41 CDT)
RE: Is it possible to perform NVT FEP on a fluid system? B.W.J. Irwin (Tue Aug 09 2016 - 11:23:58 CDT)
Is it possible to perform NVT FEP on a fluid system? B.W.J. Irwin (Tue Aug 09 2016 - 05:22:08 CDT)
Re: Energy minimization in NAMD Ajasja LjubetiÄ (Tue Aug 09 2016 - 04:24:08 CDT)
Re: Energy minimization in NAMD Ajasja LjubetiÄ (Mon Aug 08 2016 - 15:54:58 CDT)
Energy minimization in NAMD Faramarz Joodaki (Mon Aug 08 2016 - 11:37:45 CDT)
how to not overwrite a modified file? (while producing coordinates for ABF/US windows) Olya Kravchenko (Sat Aug 06 2016 - 07:18:56 CDT)
Re: How to replace NAMD Eletrostatic Forces Emerson Macedo (Fri Aug 05 2016 - 10:45:12 CDT)
Re: How to replace NAMD Eletrostatic Forces Giacomo Fiorin (Fri Aug 05 2016 - 09:45:05 CDT)
Re: How to replace NAMD Eletrostatic Forces Ajasja LjubetiÄ (Fri Aug 05 2016 - 02:46:00 CDT)
AW: How to replace NAMD Eletrostatic Forces Norman Geist (Fri Aug 05 2016 - 02:33:51 CDT)
Re: How to replace NAMD Eletrostatic Forces Brian Radak (Thu Aug 04 2016 - 15:17:17 CDT)
How to replace NAMD Eletrostatic Forces Emerson Macedo (Thu Aug 04 2016 - 13:15:38 CDT)
Re: Fatal Error: vdw atom type CC3161 Allen, Caley R (Wed Aug 03 2016 - 13:46:17 CDT)
Re: Fatal Error: vdw atom type CC3161 Chitrak Gupta (Wed Aug 03 2016 - 10:11:51 CDT)
Fatal Error: vdw atom type CC3161 Allen, Caley R (Wed Aug 03 2016 - 09:53:37 CDT)
Re: Generalized Born solvation models supported by NAMD Chitrak Gupta (Tue Aug 02 2016 - 17:54:08 CDT)
Re: Generalized Born solvation models supported by NAMD Aron Broom (Tue Aug 02 2016 - 09:41:09 CDT)
Maximum dihedral angle Mahdi Tavakol (Sun Jul 31 2016 - 03:19:16 CDT)
Re: Generalized Born solvation models supported by NAMD Chitrak Gupta (Fri Jul 29 2016 - 16:05:02 CDT)
Re: Generalized Born solvation models supported by NAMD Aron Broom (Fri Jul 29 2016 - 14:24:21 CDT)
Re: Generalized Born solvation models supported by NAMD Thomas Evangelidis (Fri Jul 29 2016 - 13:18:08 CDT)
Re: Generalized Born solvation models supported by NAMD Aron Broom (Fri Jul 29 2016 - 12:25:49 CDT)
Re: Generalized Born solvation models supported by NAMD Thomas Evangelidis (Fri Jul 29 2016 - 11:20:46 CDT)
Re: Generalized Born solvation models supported by NAMD Aron Broom (Fri Jul 29 2016 - 10:55:51 CDT)
performance drop during run Chitrak Gupta (Fri Jul 29 2016 - 10:41:32 CDT)
Generalized Born solvation models supported by NAMD Thomas Evangelidis (Fri Jul 29 2016 - 10:26:13 CDT)
water permeation through nanotube in lipid bilayer Nikhil Maroli (Fri Jul 29 2016 - 07:18:45 CDT)
Re: SMD Constant velocity pulling jeevan gc (Wed Jul 27 2016 - 16:45:19 CDT)
Re: SMD Constant velocity pulling Allen, Caley R (Wed Jul 27 2016 - 13:38:19 CDT)
group selection in TCL script for use in NAMD Allen, Caley R (Wed Jul 27 2016 - 13:35:05 CDT)
SMD Constant velocity pulling Roshan Shrestha (Wed Jul 27 2016 - 12:59:49 CDT)
Re: Kenneth Huang (Tue Jul 26 2016 - 08:09:12 CDT)
(no subject) krishna (Tue Jul 26 2016 - 00:56:38 CDT)
RE: Msd Radak, Brian K (Mon Jul 25 2016 - 12:48:13 CDT)
Re: Equivalent of gromacs' "rdd" option Marlon Sidore (Mon Jul 25 2016 - 10:44:48 CDT)
Re: Equivalent of gromacs' "rdd" option Fotis Baltoumas (Mon Jul 25 2016 - 10:26:05 CDT)
Re: Equivalent of gromacs' "rdd" option Axel Kohlmeyer (Mon Jul 25 2016 - 10:16:08 CDT)
Re: Equivalent of gromacs' "rdd" option Fotis Baltoumas (Mon Jul 25 2016 - 10:08:18 CDT)
Msd Mahdiye Azadpour (Sat Jul 23 2016 - 23:21:09 CDT)
Re: Equivalent of gromacs' "rdd" option Marlon Sidore (Mon Jul 25 2016 - 02:56:06 CDT)
Re: Problems with wrapAll Sonu Kumar (Fri Jul 22 2016 - 13:08:33 CDT)
Re: Problems with wrapAll Vermaas, Joshua (Fri Jul 22 2016 - 11:55:30 CDT)
Re: Problems with wrapAll MEHRAN MB (Fri Jul 22 2016 - 11:35:12 CDT)
Re: Equivalent of gromacs' "rdd" option Fotis Baltoumas (Fri Jul 22 2016 - 11:05:50 CDT)
Re: Equivalent of gromacs' "rdd" option Marlon Sidore (Fri Jul 22 2016 - 10:16:57 CDT)
Equivalent of gromacs' "rdd" option Marlon Sidore (Fri Jul 22 2016 - 10:12:47 CDT)
Repulsion of lipid bilayer during equilibration Mahrukh Imtiaz (Fri Jul 22 2016 - 05:00:41 CDT)
Re: Problems with wrapAll Sonu Kumar (Fri Jul 22 2016 - 06:58:13 CDT)
System temperature check of specific atoms , sys temp of only coupled atoms? Karson Bader (Thu Jul 21 2016 - 15:36:13 CDT)
is there a way to prevent ions from entering the channel? Olya Kravchenko (Thu Jul 21 2016 - 12:56:57 CDT)
Re: Problems with wrapAll Vermaas, Joshua (Thu Jul 21 2016 - 11:14:48 CDT)
Problems with wrapAll Sonu Kumar (Thu Jul 21 2016 - 00:52:55 CDT)
NAMD related theoretical questions Kostas Malavazos (Wed Jul 20 2016 - 12:33:11 CDT)
Re: Boyang Wang (Tue Jul 19 2016 - 23:33:49 CDT)
(no subject) d.ronika_at_iitg.ernet.in (Tue Jul 19 2016 - 22:52:43 CDT)
aMD doesn't work when some atoms are fixed sunyeping (Mon Jul 18 2016 - 20:41:34 CDT)
Re: how to reassign dcdfreq?? Faramarz Joodaki (Wed Jul 13 2016 - 08:02:23 CDT)
Re: how to reassign dcdfreq?? Faramarz Joodaki (Wed Jul 13 2016 - 08:01:09 CDT)
Re: how to reassign dcdfreq?? Marlon Sidore (Wed Jul 13 2016 - 03:35:52 CDT)
namd2 seg fault NAMD_2.11_Source Linux-x86_64-g++ Doug Stetner (Tue Jul 12 2016 - 22:51:40 CDT)
RE: how to reassign dcdfreq?? Radak, Brian K (Tue Jul 12 2016 - 13:22:08 CDT)
how to reassign dcdfreq?? Faramarz Joodaki (Mon Jul 11 2016 - 22:17:54 CDT)
Intramolecular interaction energy of protein in vacuum from NAMD simualtions dayanidhi mohanta (Sat Jul 09 2016 - 08:26:13 CDT)
The adaptTemp and Temp in Adaptive tempering Chenyi L (Thu Jul 07 2016 - 19:51:03 CDT)
Possible bug in DCD writer, number of frames not in NSET but in 5-ZEROS Norman Geist (Wed Jul 06 2016 - 07:26:01 CDT)
Re: unbinding free energy using ABF JC Gumbart (Tue Jul 05 2016 - 18:28:59 CDT)
Re: metadynamics and pmf file Giacomo Fiorin (Tue Jul 05 2016 - 16:29:10 CDT)
Re: vmd-l: Inconsistent atom count John Stone (Tue Jul 05 2016 - 12:54:26 CDT)
Inconsistent atom count Laura Joana (Tue Jul 05 2016 - 12:04:44 CDT)
metadynamics and pmf file Stefano Guglielmo (Mon Jul 04 2016 - 19:43:23 CDT)
Re: PMF with ABF for ion channels in a spherical molecule Aron Broom (Fri Jul 01 2016 - 18:42:21 CDT)
Re: unbinding free energy using ABF Gabriel Jara (Fri Jul 01 2016 - 16:13:32 CDT)
Re: PMF with ABF for ion channels in a spherical molecule Olya Kravchenko (Fri Jul 01 2016 - 15:50:15 CDT)
get seed Laura Joana (Fri Jul 01 2016 - 11:52:46 CDT)
Re: unbinding free energy using ABF JC Gumbart (Thu Jun 30 2016 - 15:51:09 CDT)
unbinding free energy using ABF Gabriel Jara (Thu Jun 30 2016 - 13:25:27 CDT)
Re: PMF with ABF for ion channels in a spherical molecule Aron Broom (Tue Jun 28 2016 - 16:37:49 CDT)
Re: PMF with ABF for ion channels in a spherical molecule Olya Kravchenko (Tue Jun 28 2016 - 16:20:13 CDT)
Re: PMF with ABF for ion channels in a spherical molecule Aron Broom (Tue Jun 28 2016 - 15:57:14 CDT)
Re: PMF with ABF for ion channels in a spherical molecule Olya Kravchenko (Tue Jun 28 2016 - 15:35:53 CDT)
Re: MDFF based on known EM maps Ryan McGreevy (Tue Jun 28 2016 - 12:20:46 CDT)
MDFF based on known EM maps giulia palermo (Tue Jun 28 2016 - 12:08:12 CDT)
Potential per TS looks wierd faride badalkhani (Mon Jun 27 2016 - 13:18:33 CDT)
Re: LJcorrection option in NAMD Grace Brannigan (Mon Jun 27 2016 - 06:41:33 CDT)
Re: PME vs. cutoff with switching function JC Gumbart (Mon Jun 27 2016 - 00:33:36 CDT)
Re: Tesla K80 vs 3 x GTX 980Ti JC Gumbart (Mon Jun 27 2016 - 00:26:31 CDT)
Re: LJcorrection option in NAMD JC Gumbart (Mon Jun 27 2016 - 00:23:12 CDT)
Re: PMF with ABF for ion channels in a spherical molecule Aron Broom (Sun Jun 26 2016 - 15:13:36 CDT)
Re: Tesla K80 vs 3 x GTX 980Ti Aron Broom (Sun Jun 26 2016 - 15:07:13 CDT)
Tesla K80 vs 3 x GTX 980Ti Nikhil Maroli (Sat Jun 25 2016 - 11:24:25 CDT)
Tesla K80 vs 3 x GTX 980ti Nikhil Maroli (Sat Jun 25 2016 - 08:02:25 CDT)
PMF with ABF for ion channels in a spherical molecule Olya Kravchenko (Fri Jun 24 2016 - 17:01:13 CDT)
Re: transition metal parameters luca belmonte (Fri Jun 24 2016 - 03:04:02 CDT)
transition metal parameters Francesca Lønstad Bleken (Fri Jun 24 2016 - 02:19:01 CDT)
Re: Exit Command Failure Jeff Comer (Thu Jun 23 2016 - 08:45:54 CDT)
Exit Command Failure Sarah Sweger (Thu Jun 23 2016 - 08:01:09 CDT)
The question about Network calculation ÀîÎÄ¾ê (Thu Jun 23 2016 - 03:28:47 CDT)
Re: Applying "selectionRule" in Multiple Walker ABF Souvik Sinha (Thu Jun 23 2016 - 03:07:13 CDT)
Re: LJcorrection option in NAMD Brian Radak (Wed Jun 22 2016 - 17:22:07 CDT)
Re: LJcorrection option in NAMD Brian Radak (Wed Jun 22 2016 - 17:04:02 CDT)
Re: Applying "selectionRule" in Multiple Walker ABF Marlon Sidore (Wed Jun 22 2016 - 11:00:32 CDT)
Re: Applying "selectionRule" in Multiple Walker ABF Jeff Comer (Wed Jun 22 2016 - 09:49:31 CDT)
Re: LJcorrection option in NAMD Grace Brannigan (Tue Jun 21 2016 - 13:03:24 CDT)
Re: LJcorrection option in NAMD Brian Radak (Tue Jun 21 2016 - 07:36:06 CDT)
LJcorrection option in NAMD Yue Qian (Mon Jun 20 2016 - 17:09:04 CDT)
Re: Coarse Grain Angle Parameter Issue Fotis Baltoumas (Sat Jun 18 2016 - 00:23:37 CDT)
Coarse Grain Angle Parameter Issue Nisler, Collin R. (Fri Jun 17 2016 - 22:37:42 CDT)
PME vs. cutoff with switching function Benjamin Brown (Fri Jun 17 2016 - 10:25:44 CDT)
Re: namd2 or charmrun ++local ? Giacomo Fiorin (Fri Jun 17 2016 - 13:18:48 CDT)
namd2 or charmrun ++local ? Laura Joana (Fri Jun 17 2016 - 11:35:05 CDT)
Re: RMSD faride badalkhani (Thu Jun 16 2016 - 14:13:40 CDT)
Re: RMSD Brian Radak (Thu Jun 16 2016 - 14:11:29 CDT)
Re: RMSD faride badalkhani (Thu Jun 16 2016 - 14:02:43 CDT)
Re: RMSD Brian Radak (Thu Jun 16 2016 - 13:51:46 CDT)
RMSD faride badalkhani (Thu Jun 16 2016 - 12:42:32 CDT)
Colvar orientation and CoG Nicolas Martin (Thu Jun 16 2016 - 09:02:28 CDT)
Regarding radial distribution function graph siddharth kamal (Thu Jun 16 2016 - 08:31:23 CDT)
Re: Free energy calculation using MM-GBSA with NAMD Jeff Comer (Wed Jun 15 2016 - 09:10:21 CDT)
Free energy calculation using MM-GBSA with NAMD Sneha Menon (Wed Jun 15 2016 - 05:50:41 CDT)
RE: Missing atom type for hydroperoxide Radak, Brian K (Tue Jun 14 2016 - 12:58:25 CDT)
Missing atom type for hydroperoxide Jean-FranÃ§ois Fabre (Tue Jun 14 2016 - 10:48:55 CDT)
Why does the water box collapse in an aMD sunyeping (Mon Jun 13 2016 - 21:11:00 CDT)
Re: Topology Command in VMD Josh Vermaas (Mon Jun 13 2016 - 08:22:33 CDT)
Drude Prepper error in genic Francesco Pietra (Mon Jun 13 2016 - 01:33:15 CDT)
Permeation of liquid through Silicon Dioxide Crystal Roshan Shrestha (Fri Jun 10 2016 - 07:30:00 CDT)
Topology Command in VMD Eric Weine (Thu Jun 09 2016 - 19:27:39 CDT)
The adaptTemp and Temp in Adaptive tempering §³henyi (Thu Jun 09 2016 - 15:17:25 CDT)
RE: Building PSF for the system prepared by Packmol Radak, Brian K (Thu Jun 09 2016 - 14:16:46 CDT)
Re: ATP - CGENFF JC Gumbart (Thu Jun 09 2016 - 09:36:37 CDT)
Building PSF for the system prepared by Packmol faride badalkhani (Thu Jun 09 2016 - 09:27:31 CDT)
NBFIX parameters for Calcium ion Azadeh Alavi (Thu Jun 09 2016 - 04:49:04 CDT)
ATP - CGENFF Benjamin Hill (Tue Jun 07 2016 - 19:34:15 CDT)
An script for ACF faride badalkhani (Tue Jun 07 2016 - 16:37:13 CDT)
Help about Drude Prepper Francesco Pietra (Tue Jun 07 2016 - 10:06:48 CDT)
Re: AW: Replica Exchange: Equilibrating at each temperature Horia Jalily Hasani (Tue Jun 07 2016 - 11:21:09 CDT)
cgenff Benjamin Hill (Mon Jun 06 2016 - 14:48:30 CDT)
Re: Colvars order in the pmf file Marlon Sidore (Mon Jun 06 2016 - 10:49:01 CDT)
Re: Colvars order in the pmf file Giacomo Fiorin (Mon Jun 06 2016 - 09:57:38 CDT)
Re: How can I find the proper number of solvent molecules in the simulation? Brian Radak (Mon Jun 06 2016 - 09:49:42 CDT)
How can I find the proper number of solvent molecules in the simulation? faride badalkhani (Mon Jun 06 2016 - 09:25:50 CDT)
Colvars order in the pmf file Marlon Sidore (Mon Jun 06 2016 - 09:14:53 CDT)
much larger diameter of ssDNA, Aliasghar Alizadeh-Mojarad (Sat Jun 04 2016 - 04:22:41 CDT)
namdenergy and bigdcd Grant Schauer (Thu Jun 02 2016 - 23:58:23 CDT)
Re: Unable to compile Tachyon on Sun Grid Engine Sourav Ray (Sat Jun 04 2016 - 08:03:44 CDT)
Re: Unable to compile Tachyon on Sun Grid Engine Sourav Ray (Sat Jun 04 2016 - 05:59:00 CDT)
Unable to compile Tachyon on Sun Grid Engine Sourav Ray (Sat Jun 04 2016 - 04:20:29 CDT)
Re: Is GPU double-precision floating point performance important for NAMD? Mert GÃ¼r (Fri Jun 03 2016 - 09:20:42 CDT)
AW: Is GPU double-precision floating point performance important for NAMD? Norman Geist (Fri Jun 03 2016 - 01:49:06 CDT)
AW: AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Fri Jun 03 2016 - 01:39:54 CDT)
Is GPU double-precision floating point performance important for NAMD? Mert GÃ¼r (Thu Jun 02 2016 - 16:48:07 CDT)
Re: AW: Replica Exchange: Equilibrating at each temperature Horia Jalily Hasani (Thu Jun 02 2016 - 10:59:56 CDT)
autocorrelation function faride badalkhani (Thu Jun 02 2016 - 09:06:04 CDT)
AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Thu Jun 02 2016 - 01:33:55 CDT)
download stmv files for benchmarking Bennion, Brian (Wed Jun 01 2016 - 14:29:22 CDT)
Re: Chitrak Gupta (Wed Jun 01 2016 - 13:03:34 CDT)
non-standard solvants faride badalkhani (Wed Jun 01 2016 - 11:55:28 CDT)
Re: Umbrella sampling of 2 CNT's taking distance as collective variable JÃ©rÃ´me HÃ©nin (Wed Jun 01 2016 - 10:26:27 CDT)
Re: Chitrak Gupta (Wed Jun 01 2016 - 08:57:57 CDT)
Re: Umbrella sampling of 2 CNT's taking distance as collective variable Giacomo Fiorin (Wed Jun 01 2016 - 05:07:50 CDT)
AW: Simulation runs only in background Daniel MÃ¶ller (Wed Jun 01 2016 - 04:44:55 CDT)
Re: Simulation runs only in background Marlon Sidore (Wed Jun 01 2016 - 04:09:16 CDT)
Simulation runs only in background Roshan Shrestha (Wed Jun 01 2016 - 03:44:15 CDT)
Umbrella sampling of 2 CNT's taking distance as collective variable Kashish Punjani (Wed Jun 01 2016 - 01:16:45 CDT)
(no subject) Srijita Paul (Tue May 31 2016 - 23:29:11 CDT)
Using Mergestructs Eric Weine (Tue May 31 2016 - 14:09:46 CDT)
namd "WARNING: ignoring command" problem Shambo Hore (Tue May 31 2016 - 12:11:35 CDT)
Re: Replica Exchange: Equilibrating at each temperature Horia Jalily Hasani (Tue May 31 2016 - 11:18:08 CDT)
AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Tue May 31 2016 - 08:41:23 CDT)
(no subject) Srijita Paul (Tue May 31 2016 - 05:03:47 CDT)
AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Tue May 31 2016 - 04:24:52 CDT)
Re: Applying "selectionRule" in Multiple Walker ABF Souvik Sinha (Tue May 31 2016 - 01:27:08 CDT)
Replica Exchange: Equilibrating at each temperature Horia Jalily Hasani (Mon May 30 2016 - 11:28:24 CDT)
Re: No parameter for ribose ring, Charmm 27 JC Gumbart (Mon May 30 2016 - 07:19:44 CDT)
Re: setting up simulation in vmd using charmm 36 forcefield JC Gumbart (Mon May 30 2016 - 07:29:44 CDT)
SMD simulation problem. Shambo Hore (Sun May 29 2016 - 20:15:57 CDT)
Re: No parameter for ribose ring, Charmm 27 Benjamin Hill (Sun May 29 2016 - 11:12:07 CDT)
RE: No parameter for ribose ring, Charmm 27 Lennart Nilsson (Fri May 27 2016 - 15:28:43 CDT)
Re: Conversion from GROMACS .top .itp to CHARMM .psf .par combo Roshan Shrestha (Sat May 28 2016 - 10:04:08 CDT)
Conversion from GROMACS .top .itp to CHARMM .psf .par combo Sourav Ray (Sat May 28 2016 - 10:00:54 CDT)
setting up simulation in vmd using charmm 36 forcefield Rabeta Yeasmin (Fri May 27 2016 - 16:28:38 CDT)
More FEP using separated topologies David Huggins (Fri May 27 2016 - 15:21:01 CDT)
Re: No parameter for ribose ring, Charmm 27 JC Gumbart (Fri May 27 2016 - 14:14:17 CDT)
Applying "selectionRule" in Multiple Walker ABF Souvik Sinha (Fri May 27 2016 - 09:43:28 CDT)
Re: No parameter for ribose ring, Charmm 27 Benjamin Hill (Fri May 27 2016 - 05:51:40 CDT)
No parameter for ribose ring, Charmm 27 Lennart Nilsson (Fri May 27 2016 - 05:42:02 CDT)
Re: truncated text RE: external computational power for NAMD Roshan Shrestha (Thu May 26 2016 - 21:35:39 CDT)
Re: No parameter for ribose ring, Charmm 27 JC Gumbart (Thu May 26 2016 - 18:42:52 CDT)
No parameter for ribose ring, Charmm 27 Benjamin Hill (Thu May 26 2016 - 17:18:43 CDT)
truncated text RE: external computational power for NAMD Deng, Jinxia (Nancy) (Thu May 26 2016 - 12:59:40 CDT)
external computational power for NAMD Deng, Jinxia (Nancy) (Thu May 26 2016 - 12:02:54 CDT)
Binding energy of organic molecules/small peptides on the surface of Silicon Dioxide Roshan Shrestha (Thu May 26 2016 - 10:29:01 CDT)
Re: AW: Re: AW: AW: AW: why does the transition seem to be irreversible in aMD sunyeping (Wed May 25 2016 - 00:48:18 CDT)
Re: FES analysis Giacomo Fiorin (Tue May 24 2016 - 16:00:51 CDT)
FES analysis Stefano Guglielmo (Tue May 24 2016 - 15:46:21 CDT)
hyper-branched polymers faride badalkhani (Tue May 24 2016 - 09:24:41 CDT)
Re: H-bonds in charmm36 with namd2.11 Francesco Pietra (Tue May 24 2016 - 04:30:13 CDT)
AW: Re: AW: AW: AW: why does the transition seem to be irreversible in aMD Norman Geist (Tue May 24 2016 - 00:57:09 CDT)
Re: I cannot make MD simulation constant in pressure Peter Freddolino (Mon May 23 2016 - 22:56:48 CDT)
Re: I cannot make MD simulation constant in pressure Faramarz Joodaki (Mon May 23 2016 - 22:44:21 CDT)
Re: I cannot make MD simulation constant in pressure Peter Freddolino (Mon May 23 2016 - 21:01:23 CDT)
Re: Adsorption energy of protein in vacuum Abhishek TYAGI (Mon May 23 2016 - 19:52:56 CDT)
Re: I cannot make MD simulation constant in pressure Faramarz Joodaki (Mon May 23 2016 - 18:29:14 CDT)
Re: I cannot make MD simulation constant in pressure Jeff Comer (Mon May 23 2016 - 16:06:17 CDT)
I cannot make MD simulation constant in pressure Faramarz Joodaki (Mon May 23 2016 - 14:41:54 CDT)
Re: Adsorption energy of protein in vacuum Jeff Comer (Mon May 23 2016 - 12:02:17 CDT)
namd leaves zombie processes on nodes? JC Gumbart (Mon May 23 2016 - 10:01:45 CDT)
Re: H-bonds in charmm36 with namd2.11 JC Gumbart (Mon May 23 2016 - 08:59:24 CDT)
AW: Re: AW: AW: AW: why does the transition seem to be irreversible in aMD Norman Geist (Mon May 23 2016 - 08:42:04 CDT)
firstTimestep error message Laura Joana (Mon May 23 2016 - 05:55:51 CDT)
Re: AW: AW: AW: why does the transition seem to be irreversible in aMD sunyeping (Mon May 23 2016 - 03:53:37 CDT)
Re: Restart multiple walker ABF Atanu Maity (Mon May 23 2016 - 01:13:10 CDT)
Re: Restart multiple walker ABF Atanu Maity (Sun May 22 2016 - 23:55:32 CDT)
Re: Adsorption energy of protein in vacuum Abhishek TYAGI (Sun May 22 2016 - 22:46:38 CDT)
RE: Parameters for HS(CH2)11NH2 Deng, Jinxia (Nancy) (Sun May 22 2016 - 14:03:37 CDT)
Re: SMD simulation problem Madhulika Gupta (Sun May 22 2016 - 10:59:18 CDT)
SMD simulation problem Shambo Hore (Sun May 22 2016 - 10:37:52 CDT)
Fwd: H-bonds in charmm36 with namd2.11 Francesco Pietra (Sun May 22 2016 - 01:46:52 CDT)
Re: H-bonds in charmm36 with namd2.11 Francesco Pietra (Sun May 22 2016 - 01:43:55 CDT)
Re: H-bonds in charmm36 with namd2.11 JC Gumbart (Sat May 21 2016 - 18:44:09 CDT)
Re: Coarse-grained simulation with Polarizable Water crashing Fotis Baltoumas (Sat May 21 2016 - 17:14:36 CDT)
Re: Coarse-grained simulation with Polarizable Water crashing Sourav Ray (Sat May 21 2016 - 11:39:42 CDT)
Re: Adsorption energy of protein in vacuum Madhulika Gupta (Sat May 21 2016 - 10:20:34 CDT)
Re: Adsorption energy of protein in vacuum Ana Celia Vila Verde (Sat May 21 2016 - 04:17:54 CDT)
Parameters for HS(CH2)11NH2 Natnael Doilicho (Fri May 20 2016 - 19:06:55 CDT)
H-bonds in charmm36 with namd2.11 Francesco Pietra (Fri May 20 2016 - 16:18:22 CDT)
Have GPU-accelerated NAMD Questions? Join us for a Live Webinar MARK (Fri May 20 2016 - 13:07:08 CDT)
RE: Excessively high dE_avg values in FEP output (NAMD CVS) Radak, Brian K (Fri May 20 2016 - 11:58:43 CDT)
Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Pardis Tabaee (Fri May 20 2016 - 11:12:24 CDT)
Re: Some questions on the Deca-Alanine ABF tutorial Pardis Tabaee (Fri May 20 2016 - 09:52:09 CDT)
Re: Colvars: Unable to restrict rotation and translation along y and z axes Giacomo Fiorin (Fri May 20 2016 - 10:33:27 CDT)
Re: Some questions on the Deca-Alanine ABF tutorial Pardis Tabaee (Fri May 20 2016 - 10:01:13 CDT)
Re: Excessively high dE_avg values in FEP output (NAMD CVS) Brian Radak (Fri May 20 2016 - 07:47:33 CDT)
Adsorption energy of protein in vacuum Madhulika Gupta (Fri May 20 2016 - 06:01:05 CDT)
Re: Colvars: Unable to restrict rotation and translation along y and z axes Sourav Ray (Fri May 20 2016 - 01:31:38 CDT)
Re: Some questions on the Deca-Alanine ABF tutorial sunyeping (Thu May 19 2016 - 22:41:05 CDT)
Re: Excessively high dE_avg values in FEP output (NAMD CVS) Reza Salari (Thu May 19 2016 - 16:21:08 CDT)
Re: Restart multiple walker ABF Jeff Comer (Thu May 19 2016 - 15:58:22 CDT)
Re: Restart multiple walker ABF Atanu Maity (Thu May 19 2016 - 03:36:30 CDT)
Restart multiple walker ABF Atanu Maity (Thu May 19 2016 - 03:32:24 CDT)
Re: Some questions on the Deca-Alanine ABF tutorial sunyeping (Wed May 18 2016 - 20:29:46 CDT)
Re: TIP4P water with flexible bonds Jeff Comer (Wed May 18 2016 - 17:03:53 CDT)
TIP4P water with flexible bonds Hartling, Kathryn (Wed May 18 2016 - 14:32:24 CDT)
Re: Excessively high dE_avg values in FEP output (NAMD CVS) Brian Radak (Wed May 18 2016 - 13:25:44 CDT)
Re: Colvars: Unable to restrict rotation and translation along y and z axes Giacomo Fiorin (Wed May 18 2016 - 08:23:14 CDT)
Colvars: Unable to restrict rotation and translation along y and z axes Sourav Ray (Wed May 18 2016 - 07:22:00 CDT)
Re: Some questions on the Deca-Alanine ABF tutorial sunyeping (Wed May 18 2016 - 03:06:08 CDT)
MDFF with two symmetry groups Benjamin.Haberl_at_physik.uni-muenchen.de (Tue May 17 2016 - 14:48:19 CDT)
Re: Excessively high dE_avg values in FEP output (NAMD CVS) Reza Salari (Tue May 17 2016 - 14:20:32 CDT)
Error associated with protected variable initialization: Nightly Build version Sourav Ray (Tue May 17 2016 - 13:50:54 CDT)
Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Tue May 17 2016 - 11:43:05 CDT)
Ph.D. positions available Ivaylo Nikolaev Ivanov (Tue May 17 2016 - 10:10:41 CDT)
Postdoc position available Ivaylo Nikolaev Ivanov (Tue May 17 2016 - 10:05:18 CDT)
Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params JC Gumbart (Tue May 17 2016 - 09:29:52 CDT)
ffTK fitting dihedrals Seth Axen (Tue May 17 2016 - 01:36:02 CDT)
Re: Excessively high dE_avg values in FEP output (NAMD CVS) Giacomo Fiorin (Mon May 16 2016 - 18:51:55 CDT)
running simulations in successive steps faride badalkhani (Mon May 16 2016 - 17:31:31 CDT)
Excessively high dE_avg values in FEP output (NAMD CVS) Reza Salari (Mon May 16 2016 - 16:29:32 CDT)
Combining Drude structures Jeff Comer (Mon May 16 2016 - 16:25:32 CDT)
Re: Coarse-grained simulation with Polarizable Water crashing Sourav Ray (Mon May 16 2016 - 15:31:14 CDT)
Excessively high dE_avg values in FEP output (NAMD CVS) Reza Salari (Mon May 16 2016 - 12:42:27 CDT)
Re: Coarse-grained simulation with Polarizable Water crashing Jeff Comer (Mon May 16 2016 - 12:04:43 CDT)
Particle Mesh Ewald with Martini Sourav Ray (Mon May 16 2016 - 10:55:14 CDT)
Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Mon May 16 2016 - 08:54:45 CDT)
Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Mon May 16 2016 - 08:54:31 CDT)
Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Peter Freddolino (Mon May 16 2016 - 07:46:47 CDT)
Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Mon May 16 2016 - 04:30:29 CDT)
Some questions on the Deca-Alanine ABF tutorial sunyeping (Mon May 16 2016 - 04:19:33 CDT)
Re: Equilibration and production run Ajasja LjubetiÄ (Mon May 16 2016 - 03:23:29 CDT)
CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Mon May 16 2016 - 02:45:55 CDT)
Equilibration and production run dhirajks_at_gmail.com (Mon May 16 2016 - 01:25:32 CDT)
Re: Coarse-grained simulation with Polarizable Water crashing Sourav Ray (Sun May 15 2016 - 17:08:31 CDT)
Coarse-grained simulation with Polarizable Water crashing Sourav Ray (Sun May 15 2016 - 16:34:18 CDT)
Re: Conversion from c6 and c12 = 0 to sigma epsilon Brian Radak (Sat May 14 2016 - 15:39:48 CDT)
Conversion from c6 and c12 = 0 to sigma epsilon Sourav Ray (Sat May 14 2016 - 06:29:49 CDT)
Output temperature not agreeing with tcouple temperature Karson Bader (Fri May 13 2016 - 12:07:52 CDT)
Martini polarizable water topology and/or psf file Sourav Ray (Thu May 12 2016 - 17:30:57 CDT)
Re: Colvars crossing "upperboundary" limit Giacomo Fiorin (Tue May 10 2016 - 15:25:18 CDT)
Re: Chitrak Gupta (Tue May 10 2016 - 13:57:03 CDT)
PMF calculation using ABF Souvik Sinha (Tue May 10 2016 - 08:57:52 CDT)
Re: Srijita Paul (Tue May 10 2016 - 08:41:10 CDT)
Re: Chitrak Gupta (Mon May 09 2016 - 11:07:14 CDT)
RE: gradual heating problem Radak, Brian K (Mon May 09 2016 - 10:12:01 CDT)
Re: Maxim Belkin (Mon May 09 2016 - 09:38:23 CDT)
PMEProcessors setting on one node dhirajks_at_gmail.com (Sun May 08 2016 - 21:22:54 CDT)
Re: Jeff Comer (Sun May 08 2016 - 20:19:44 CDT)
Re: gradual heating problem dhirajks_at_gmail.com (Sun May 08 2016 - 11:21:13 CDT)
Re: gradual heating problem Brian Radak (Sun May 08 2016 - 11:04:31 CDT)
gradual heating problem Dhiraj Srivastava (Sun May 08 2016 - 10:27:39 CDT)
Re: Abhishek TYAGI (Sat May 07 2016 - 07:45:54 CDT)
(no subject) Srijita Paul (Sat May 07 2016 - 06:17:48 CDT)
RE: heating in NPT ensemble Radak, Brian K (Fri May 06 2016 - 10:04:07 CDT)
Re: LJ parameters for Pd surface Axel Kohlmeyer (Fri May 06 2016 - 08:36:59 CDT)
LJ parameters for Pd surface Madhulika Gupta (Fri May 06 2016 - 08:33:03 CDT)
Re: Problem with the cross term of C NH1 CT1 C NH1 CT1 C NH1 Pardis Tabaee (Fri May 06 2016 - 08:05:10 CDT)
heating in NPT ensemble Dhiraj Srivastava (Thu May 05 2016 - 17:39:35 CDT)
NAMD Recipe for Success with GPUs! MARK (Thu May 05 2016 - 11:35:42 CDT)
Colvars crossing "upperboundary" limit Sourav Ray (Thu May 05 2016 - 05:33:26 CDT)
Recipe for Success - GPU accelerated NAMD Mark Berger (Wed May 04 2016 - 19:25:24 CDT)
Re: excluding non-bonded interactions between two proteins Peter Freddolino (Wed May 04 2016 - 19:14:34 CDT)
Re: excluding non-bonded interactions between two proteins JC Gumbart (Wed May 04 2016 - 19:04:43 CDT)
Re: excluding non-bonded interactions between two proteins Peter Freddolino (Wed May 04 2016 - 18:41:18 CDT)
excluding non-bonded interactions between two proteins JC Gumbart (Wed May 04 2016 - 18:16:26 CDT)
parameterization of cations faride badalkhani (Wed May 04 2016 - 11:28:59 CDT)
Re: WHY!!! num_runs should be divisible by runs_per_frame * frames_per_restart -->REMD Nicholus Bhattacharjee (Wed May 04 2016 - 10:07:53 CDT)
Re: WHY!!! num_runs should be divisible by runs_per_frame * frames_per_restart -->REMD Peter Freddolino (Tue May 03 2016 - 11:08:17 CDT)
parameterizing a new solvent faride badalkhani (Tue May 03 2016 - 08:54:06 CDT)
Re: TCL Scripting for Force Calculations Allen, Caley R (Mon May 02 2016 - 14:08:17 CDT)
Re: water box and padding Jeff Comer (Mon May 02 2016 - 11:10:45 CDT)
TCL Scripting for Force Calculations Allen, Caley R (Mon May 02 2016 - 10:48:56 CDT)
Re: water box and padding Brian Radak (Mon May 02 2016 - 09:54:43 CDT)
Re: unix path length limits for namd Shyam Saladi (Sun May 01 2016 - 19:21:27 CDT)
unix path length limits for namd Chris Goedde (Sun May 01 2016 - 17:10:34 CDT)
water box and padding Dhiraj Srivastava (Sat Apr 30 2016 - 11:40:53 CDT)
Compilation of NAMD for CUDA and replica exchange #YEO JINGJIE# (Fri Apr 29 2016 - 13:53:44 CDT)
Re: Re: accessing values of 'extendedLagrangian' fictious degree of freedom JÃ©rÃ´me HÃ©nin (Fri Apr 29 2016 - 04:37:36 CDT)
Dihedral missing faride badalkhani (Thu Apr 28 2016 - 17:54:15 CDT)
Re: restart file - langevin options removed? Olya Kravchenko (Thu Apr 28 2016 - 15:59:09 CDT)
Re: restart file - langevin options removed? Maxim Belkin (Thu Apr 28 2016 - 15:36:52 CDT)
Re: restart file - langevin options removed? Olya Kravchenko (Thu Apr 28 2016 - 15:28:57 CDT)
Re: restart file - langevin options removed? Maxim Belkin (Thu Apr 28 2016 - 15:17:35 CDT)
Re: restart file - langevin options removed? Josh Vermaas (Thu Apr 28 2016 - 15:16:41 CDT)
Re: restart file - langevin options removed? Olya Kravchenko (Thu Apr 28 2016 - 15:13:00 CDT)
Re: restart file - langevin options removed? Maxim Belkin (Thu Apr 28 2016 - 15:00:57 CDT)
restart file - langevin options removed? Olya Kravchenko (Thu Apr 28 2016 - 14:49:45 CDT)
Re: accessing values of 'extendedLagrangian' fictious degree of freedom Prabhakar Bhimalapuram (Thu Apr 28 2016 - 12:23:36 CDT)
Re: Running a test simulation using GPU only (without any CPU core) Axel Kohlmeyer (Thu Apr 28 2016 - 10:40:38 CDT)
Re: Running a test simulation using GPU only (without any CPU core) Josh Vermaas (Thu Apr 28 2016 - 10:09:28 CDT)
minimization, heating, equilibration and production run in one script Dhiraj Srivastava (Thu Apr 28 2016 - 10:05:55 CDT)
Re: Running a test simulation using GPU only (without any CPU core) Sourav Ray (Thu Apr 28 2016 - 10:04:29 CDT)
Re: Running a test simulation using GPU only (without any CPU core) Brian Radak (Thu Apr 28 2016 - 10:00:42 CDT)
Running a test simulation using GPU only (without any CPU core) Sourav Ray (Thu Apr 28 2016 - 09:40:00 CDT)
Re: Autoionize and topology Josh Vermaas (Wed Apr 27 2016 - 08:11:15 CDT)
Re: accessing values of 'extendedLagrangian' fictious degree of freedom JÃ©rÃ´me HÃ©nin (Wed Apr 27 2016 - 04:24:18 CDT)
Autoionize and topology Dhiraj Srivastava (Tue Apr 26 2016 - 22:07:04 CDT)
accessing values of 'extendedLagrangian' fictious degree of freedom Prabhakar Bhimalapuram (Tue Apr 26 2016 - 22:01:58 CDT)
Re: CHARMM36 and TIP3 Josh Vermaas (Tue Apr 26 2016 - 19:49:04 CDT)
Re: CHARMM36 and TIP3 Dhiraj Srivastava (Tue Apr 26 2016 - 17:01:10 CDT)
Re: Constraint failure in RATTLE algorithm for atom 6! faride badalkhani (Tue Apr 26 2016 - 16:47:59 CDT)
Re: Constraint failure in RATTLE algorithm for atom 6! faride badalkhani (Tue Apr 26 2016 - 16:46:40 CDT)
RE: Constraint failure in RATTLE algorithm for atom 6! Radak, Brian K (Tue Apr 26 2016 - 16:40:45 CDT)
RE: Constraint failure in RATTLE algorithm for atom 6! Bennion, Brian (Tue Apr 26 2016 - 16:29:09 CDT)
RE: Constraint failure in RATTLE algorithm for atom 6! Radak, Brian K (Tue Apr 26 2016 - 16:26:30 CDT)
Re: Constraint failure in RATTLE algorithm for atom 6! faride badalkhani (Tue Apr 26 2016 - 16:22:02 CDT)
Re: Constraint failure in RATTLE algorithm for atom 6! Jeff Comer (Tue Apr 26 2016 - 16:14:50 CDT)
Re: CHARMM36 and TIP3 Brian Radak (Tue Apr 26 2016 - 13:57:05 CDT)
CHARMM36 and TIP3 Dhiraj Srivastava (Tue Apr 26 2016 - 13:37:49 CDT)
Re: Alchemify Possibilities David Huggins (Tue Apr 26 2016 - 09:28:15 CDT)
Amino acid as ligand Dhiraj Srivastava (Mon Apr 25 2016 - 12:22:24 CDT)
Re: Alchemify Possibilities Brian Radak (Mon Apr 25 2016 - 11:15:19 CDT)
Alchemify Possibilities David Huggins (Mon Apr 25 2016 - 11:03:10 CDT)
Constraint failure in RATTLE algorithm for atom 6! faride badalkhani (Mon Apr 25 2016 - 10:42:52 CDT)
XPLOR format PSF file for small molecules Felix W.-H. Weng (Sun Apr 24 2016 - 11:21:45 CDT)
Re: Why wrapped and unwrapped trajectories show different energies over the time? Brian Radak (Sun Apr 24 2016 - 09:03:07 CDT)
Re: Why wrapped and unwrapped trajectories show different energies over the time? Jason Swails (Sun Apr 24 2016 - 00:23:50 CDT)
Re: Chitrak Gupta (Sat Apr 23 2016 - 23:19:09 CDT)
Why wrapped and unwrapped trajectories show different energies over the time? zeynab hoseyni (Sat Apr 23 2016 - 21:22:04 CDT)
Why wrapped and unwrapped trajectories show different energies over time? zeynab mohamad hoseyni (Sat Apr 23 2016 - 09:30:08 CDT)
SMD in NAMD Madhulika Gupta (Sat Apr 23 2016 - 05:15:34 CDT)
Re: Peter Freddolino (Fri Apr 22 2016 - 12:26:51 CDT)
WHY!!! num_runs should be divisible by runs_per_frame * frames_per_restart -->REMD Nicholus Bhattacharjee (Fri Apr 22 2016 - 08:21:46 CDT)
Re: Srijita Paul (Fri Apr 22 2016 - 05:39:12 CDT)
Re: Replica exchange arpita agarwal (Fri Apr 22 2016 - 02:54:50 CDT)
Re: Akshay Bhatnagar (Fri Apr 22 2016 - 02:30:13 CDT)
(no subject) Srijita Paul (Fri Apr 22 2016 - 01:19:21 CDT)
Replica exchange arpita agarwal (Thu Apr 21 2016 - 00:43:44 CDT)
RE: How to use a proper force constant to decrease computational cost while keeping calculation precision? Radak, Brian K (Wed Apr 20 2016 - 16:22:09 CDT)
cell basis vectors faride badalkhani (Wed Apr 20 2016 - 13:59:11 CDT)
Re: rotation angle Giacomo Fiorin (Wed Apr 20 2016 - 13:51:43 CDT)
rotation angle giulia palermo (Wed Apr 20 2016 - 12:25:16 CDT)
Re: How to use a proper force constant to decrease computational cost while keeping calculation precision? Ana Celia Vila Verde (Wed Apr 20 2016 - 03:03:08 CDT)
How to use a proper force constant to decrease computational cost while keeping calculation precision? wliu (Wed Apr 20 2016 - 02:18:01 CDT)
Re: Peter Freddolino (Tue Apr 19 2016 - 10:03:52 CDT)
simulation of hyperbranched polymers faride badalkhani (Tue Apr 19 2016 - 07:54:49 CDT)
clarification sem ciccioni (Mon Apr 18 2016 - 16:21:08 CDT)
Early bird extended! ISQBP2016 meeting - Bergen Norway Vlad Cojocaru (Mon Apr 18 2016 - 14:35:38 CDT)
initial structure faride badalkhani (Mon Apr 18 2016 - 10:17:30 CDT)
Re: ERROR: ofstream_namd::close() called when file is not open Giacomo Fiorin (Mon Apr 18 2016 - 07:36:01 CDT)
Re: ERROR: ofstream_namd::close() called when file is not open Souvik Sinha (Mon Apr 18 2016 - 06:54:37 CDT)
Re: ERROR: ofstream_namd::close() called when file is not open Giacomo Fiorin (Mon Apr 18 2016 - 06:40:09 CDT)
ERROR: ofstream_namd::close() called when file is not open Souvik Sinha (Mon Apr 18 2016 - 02:36:33 CDT)
Re: Peter Freddolino (Sat Apr 16 2016 - 20:14:41 CDT)
(no subject) Srijita Paul (Sat Apr 16 2016 - 00:06:47 CDT)
initial structure faride badalkhani (Fri Apr 15 2016 - 14:18:03 CDT)
NAMD Developer Workshop: May 26-27 in Chicago, IL Jodi Ann Hadden (Fri Apr 15 2016 - 13:14:22 CDT)
Re: Dynamics of an interface Water/Hexane Maxim Belkin (Fri Apr 15 2016 - 07:39:43 CDT)
Re: Corrfunc output not generated Giacomo Fiorin (Thu Apr 14 2016 - 17:41:44 CDT)
Bad initial structure? faride badalkhani (Thu Apr 14 2016 - 13:50:14 CDT)
Re: Polymer moves to the edge of water box during the simulation faride badalkhani (Thu Apr 14 2016 - 09:56:07 CDT)
Sugar phosphate topology and parameter Dhiraj Srivastava (Thu Apr 14 2016 - 00:32:55 CDT)
Regarding Bionanotechnology tutorial arpita agarwal (Wed Apr 13 2016 - 20:07:26 CDT)
Re: Polymer moves to the edge of water box during the simulation faride badalkhani (Wed Apr 13 2016 - 12:55:28 CDT)
Re: Dynamics of an interface Water/Hexane Amy Rice (Wed Apr 13 2016 - 11:32:09 CDT)
Re: Polymer moves to the edge of water box during the simulation faride badalkhani (Wed Apr 13 2016 - 08:32:29 CDT)
Re: Jeff Comer (Wed Apr 13 2016 - 08:32:23 CDT)
Re: Polymer moves to the edge of water box during the simulation Josh Vermaas (Wed Apr 13 2016 - 08:02:36 CDT)
Dynamics of an interface Water/Hexane Jean-FranÃ§ois Fabre (Wed Apr 13 2016 - 07:54:17 CDT)
(no subject) Srijita Paul (Wed Apr 13 2016 - 07:08:28 CDT)
Re: Corrfunc output not generated Giacomo Fiorin (Tue Apr 12 2016 - 22:00:04 CDT)
Re: Polymer moves to the edge of water box during the simulation faride badalkhani (Tue Apr 12 2016 - 17:02:19 CDT)
Re: Polymer moves to the edge of water box during the simulation Josh Vermaas (Tue Apr 12 2016 - 16:54:35 CDT)
Polymer moves to the edge of water box during the simulation faride badalkhani (Tue Apr 12 2016 - 16:49:21 CDT)
Re: Corrfunc output not generated Giacomo Fiorin (Tue Apr 12 2016 - 16:16:00 CDT)
Unexpected(?) callback behavior when minimizing before MD Radak, Brian K (Tue Apr 12 2016 - 16:02:34 CDT)
Re: Few doubt on the numbers implying in REMD simulation Chitrak Gupta (Tue Apr 12 2016 - 10:00:21 CDT)
Re: Jeff Comer (Tue Apr 12 2016 - 08:56:29 CDT)
(no subject) Srijita Paul (Tue Apr 12 2016 - 07:33:41 CDT)
Few doubt on the numbers implying in REMD simulation Nicholus Bhattacharjee (Tue Apr 12 2016 - 07:06:42 CDT)
Corrfunc output not generated Sourav Ray (Mon Apr 11 2016 - 12:38:39 CDT)
Re: Metadynamics simulation with Radius of Gyration and RMSD variation - 2 Sourav Ray (Mon Apr 11 2016 - 11:10:57 CDT)
Re: Metadynamics simulation with Radius of Gyration and RMSD variation - 2 Giacomo Fiorin (Mon Apr 11 2016 - 10:08:14 CDT)
Re: Metadynamics simulation with Radius of Gyration and RMSD variation - 1 Giacomo Fiorin (Mon Apr 11 2016 - 10:02:45 CDT)
Ru surface potential Madhulika Gupta (Mon Apr 11 2016 - 03:52:26 CDT)
Re: Metadynamics simulation with Radius of Gyration and RMSD variation - 2 Sourav Ray (Sat Apr 09 2016 - 14:53:15 CDT)
Metadynamics simulation with Radius of Gyration and RMSD variation - 2 Sourav Ray (Sat Apr 09 2016 - 12:11:53 CDT)
Metadynamics simulation with Radius of Gyration and RMSD variation - 1 Sourav Ray (Sat Apr 09 2016 - 12:03:36 CDT)
Running Charmm36 Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Fri Apr 08 2016 - 19:04:49 CDT)
Re: Chitrak Gupta (Fri Apr 08 2016 - 16:40:46 CDT)
Re: LJ Parameters for Au and S and harmonic constraints Jeff Comer (Fri Apr 08 2016 - 12:52:50 CDT)
Re: Chitrak Gupta (Fri Apr 08 2016 - 10:01:07 CDT)
(no subject) Srijita Paul (Fri Apr 08 2016 - 08:00:25 CDT)
Re: LJ Parameters for Au and S and harmonic constraints Madhulika Gupta (Fri Apr 08 2016 - 03:24:34 CDT)
Re: LJ Parameters for Au and S and harmonic constraints Ana Celia Vila Verde (Fri Apr 08 2016 - 02:55:45 CDT)
LJ Parameters for Au and S and harmonic constraints Madhulika Gupta (Fri Apr 08 2016 - 02:18:29 CDT)
Re: Simulated annealing error Brian Radak (Thu Apr 07 2016 - 15:34:51 CDT)
Simulated annealing error faride badalkhani (Thu Apr 07 2016 - 13:13:38 CDT)
Packing of different system Srijita Paul (Thu Apr 07 2016 - 10:51:32 CDT)
Re: simulated annealing Brian Radak (Thu Apr 07 2016 - 10:00:03 CDT)
simulated annealing faride badalkhani (Thu Apr 07 2016 - 08:14:10 CDT)
Few doubt on the numbers implying in REMD simulatio Nicholus Bhattacharjee (Thu Apr 07 2016 - 03:34:44 CDT)
Re: restart a job Ana Celia Vila Verde (Thu Apr 07 2016 - 02:43:32 CDT)
Re: water box has a weird shape Ana Celia Vila Verde (Thu Apr 07 2016 - 02:40:47 CDT)
FEP/REMD with NAMD2.11 - missing alchLambda? Nathan Lim (Wed Apr 06 2016 - 20:42:58 CDT)
Re: water box has a weird shape Aron Broom (Wed Apr 06 2016 - 13:41:04 CDT)
water box has a weird shape faride badalkhani (Wed Apr 06 2016 - 13:21:28 CDT)
Re: restart a job Life Sciences Inc (Wed Apr 06 2016 - 12:40:28 CDT)
restart a job Farideh Badalkhani Khamseh (Wed Apr 06 2016 - 11:57:49 CDT)
simulated annealing faride badalkhani (Wed Apr 06 2016 - 11:24:30 CDT)
Re: Lowe-Andersen, Langevin and velocity rescaling thermostats (lipid bilayers) Jeff Comer (Wed Apr 06 2016 - 08:49:16 CDT)
Post Doctoral Fellow Opening at IBM for Biomolecular Modeling Tien Huynh (Tue Apr 05 2016 - 18:30:43 CDT)
Re: AW: problem with +devices using nikolaev_at_spbau.ru (Tue Apr 05 2016 - 07:41:17 CDT)
Re: Constraint failure in RATTLE algorithm for atom 538 Chitrak Gupta (Tue Apr 05 2016 - 11:04:08 CDT)
Re: Constraint failure in RATTLE algorithm for atom 538 Olya Kravchenko (Tue Apr 05 2016 - 10:29:38 CDT)
Re: Constraint failure in RATTLE algorithm for atom 538 faride badalkhani (Tue Apr 05 2016 - 10:18:25 CDT)
Re: Constraint failure in RATTLE algorithm for atom 538 Chitrak Gupta (Tue Apr 05 2016 - 10:10:44 CDT)
Re: Constraint failure in RATTLE algorithm for atom 538 Brian Radak (Tue Apr 05 2016 - 10:04:40 CDT)
Few doubt on the numbers implying in REMD simulation Nicholus Bhattacharjee (Tue Apr 05 2016 - 10:00:50 CDT)
Constraint failure in RATTLE algorithm for atom 538 faride badalkhani (Tue Apr 05 2016 - 09:57:30 CDT)
Re: AW: AW: AW: why does the transition seem to be irreversible in aMD Brian Radak (Tue Apr 05 2016 - 09:42:27 CDT)
AW: AW: problem with +devices using Norman Geist (Tue Apr 05 2016 - 08:21:37 CDT)
AW: problem with +devices using Norman Geist (Tue Apr 05 2016 - 07:09:22 CDT)
problem with +devices using nikolaev_at_spbau.ru (Tue Apr 05 2016 - 06:35:23 CDT)
AW: AW: AW: why does the transition seem to be irreversible in aMD Norman Geist (Tue Apr 05 2016 - 04:31:27 CDT)
Re: AW: AW: why does the transition seem to be irreversible in aMD sunyeping (Tue Apr 05 2016 - 04:10:59 CDT)
AW: AW: why does the transition seem to be irreversible in aMD Norman Geist (Tue Apr 05 2016 - 03:06:43 CDT)
Re: AW: why does the transition seem to be irreversible in aMD sunyeping (Tue Apr 05 2016 - 02:47:39 CDT)
AW: why does the transition seem to be irreversible in aMD Norman Geist (Tue Apr 05 2016 - 02:29:42 CDT)
Re: Running multi-node jobs on Sun Grid Engine Sourav Ray (Tue Apr 05 2016 - 00:19:23 CDT)
why does the transition seem to be irreversible in aMD sunyeping (Mon Apr 04 2016 - 22:21:00 CDT)
Re: Dihedral parameter missing Josh Vermaas (Mon Apr 04 2016 - 16:30:27 CDT)
Dihedral parameter missing faride badalkhani (Mon Apr 04 2016 - 16:26:03 CDT)
Re: Stray PME grid charges detected Sourav Ray (Mon Apr 04 2016 - 13:12:41 CDT)
Re: Stray PME grid charges detected faride badalkhani (Mon Apr 04 2016 - 13:02:51 CDT)
Re: Lowe-Andersen, Langevin and velocity rescaling thermostats (lipid bilayers) Brian Radak (Mon Apr 04 2016 - 09:44:37 CDT)
Wrapping molecules in a NAMD simulation Sourav Ray (Mon Apr 04 2016 - 08:23:02 CDT)
Lowe-Andersen, Langevin and velocity rescaling thermostats (lipid bilayers) Loison Claire (Mon Apr 04 2016 - 07:16:22 CDT)
AW: Running multi-node jobs on Sun Grid Engine Norman Geist (Mon Apr 04 2016 - 05:32:12 CDT)
Re: Stray PME grid charges detected Sourav Ray (Mon Apr 04 2016 - 05:26:56 CDT)
Re: Running multi-node jobs on Sun Grid Engine Sourav Ray (Mon Apr 04 2016 - 04:39:57 CDT)
AW: Running multi-node jobs on Sun Grid Engine Norman Geist (Mon Apr 04 2016 - 01:50:27 CDT)
AW: Occasional performance slow down using NAMD with Xeon Phi Norman Geist (Mon Apr 04 2016 - 01:47:27 CDT)
Stray PME grid charges detected faride badalkhani (Sun Apr 03 2016 - 12:49:18 CDT)
Re: Running multi-node jobs on Sun Grid Engine Ã‰ric Germaneau (Sun Apr 03 2016 - 20:34:20 CDT)
Running multi-node jobs on Sun Grid Engine Sourav Ray (Sun Apr 03 2016 - 10:49:30 CDT)
Re: Steered MD diminishing distances Giacomo Fiorin (Sat Apr 02 2016 - 20:56:34 CDT)
Steered MD diminishing distances giulia palermo (Sat Apr 02 2016 - 20:29:14 CDT)
Re: maximum coordinate is negative for z faride badalkhani (Fri Apr 01 2016 - 12:23:38 CDT)
Re: maximum coordinate is negative for z Maxim Belkin (Fri Apr 01 2016 - 12:21:05 CDT)
Re: maximum coordinate is negative for z Aron Broom (Fri Apr 01 2016 - 12:16:52 CDT)
maximum coordinate is negative for z faride badalkhani (Fri Apr 01 2016 - 12:14:17 CDT)
Re: "Jump" in Energy and Volume graphs of my MD David Hardy (Fri Apr 01 2016 - 12:09:44 CDT)
Occasional performance slow down using NAMD with Xeon Phi Mattia Felice Palermo (Fri Apr 01 2016 - 09:53:37 CDT)
Re: Making NAMD aware of Tcl packages? Brian Radak (Thu Mar 31 2016 - 16:12:20 CDT)
Re: Making NAMD aware of Tcl packages? Giacomo Fiorin (Thu Mar 31 2016 - 11:36:20 CDT)
Re: "Jump" in Energy and Volume graphs of my MD Daniela Rivas (Thu Mar 31 2016 - 11:21:03 CDT)
Re: Making NAMD aware of Tcl packages? Brian Radak (Thu Mar 31 2016 - 10:20:42 CDT)
Re: Making NAMD aware of Tcl packages? Giacomo Fiorin (Thu Mar 31 2016 - 10:17:30 CDT)
Making NAMD aware of Tcl packages? Brian Radak (Thu Mar 31 2016 - 10:11:07 CDT)
Re: "Jump" in Energy and Volume graphs of my MD Peter Freddolino (Thu Mar 31 2016 - 09:13:46 CDT)
Re: AW: "Jump" in Energy and Volume graphs of my MD Jeff Comer (Thu Mar 31 2016 - 08:44:50 CDT)
Re: AW: "Jump" in Energy and Volume graphs of my MD Brian Radak (Thu Mar 31 2016 - 07:56:32 CDT)
constant velocity pulling Jamal Zanjani (Thu Mar 31 2016 - 06:04:18 CDT)
AW: "Jump" in Energy and Volume graphs of my MD Norman Geist (Thu Mar 31 2016 - 01:00:46 CDT)
Re: "Jump" in Energy and Volume graphs of my MD Peter Freddolino (Wed Mar 30 2016 - 19:33:49 CDT)
segmentation fault (core dumped) faride badalkhani (Wed Mar 30 2016 - 16:24:26 CDT)
Re: "Jump" in Energy and Volume graphs of my MD Peter Freddolino (Wed Mar 30 2016 - 15:56:22 CDT)
Re: "Jump" in Energy and Volume graphs of my MD Daniela Rivas (Wed Mar 30 2016 - 15:49:01 CDT)
Re: "Jump" in Energy and Volume graphs of my MD Peter Freddolino (Wed Mar 30 2016 - 15:23:46 CDT)
"Jump" in Energy and Volume graphs of my MD Daniela Rivas (Wed Mar 30 2016 - 15:04:07 CDT)
RE: problem with angle parameters Radak, Brian K (Wed Mar 30 2016 - 11:09:12 CDT)
Fwd: problem with angle parameters faride badalkhani (Wed Mar 30 2016 - 10:01:22 CDT)
problem with angle parameters faride badalkhani (Wed Mar 30 2016 - 09:01:20 CDT)
Re: size of water box and cellbasisvectors Ajasja LjubetiÄ (Wed Mar 30 2016 - 08:08:14 CDT)
size of water box and cellbasisvectors faride badalkhani (Wed Mar 30 2016 - 07:51:14 CDT)
Re: Mixing all_36_cgenff with all_36_prot Tristan Croll (Mon Mar 28 2016 - 14:36:33 CDT)
Mixing all_36_cgenff with all_36_prot Francesco Pietra (Sat Mar 26 2016 - 13:02:27 CDT)
Re: varying two colvar distances simultaneously Giacomo Fiorin (Fri Mar 25 2016 - 17:22:37 CDT)
Re: varying two colvar distances simultaneously Chitrak Gupta (Fri Mar 25 2016 - 17:20:57 CDT)
Re: force units conversion Maxim Belkin (Fri Mar 25 2016 - 14:12:22 CDT)
Re: varying two colvar distances simultaneously Chitrak Gupta (Fri Mar 25 2016 - 10:58:08 CDT)
Re: force units conversion Maxim Belkin (Fri Mar 25 2016 - 10:42:40 CDT)
HBB2-pol R. Charbel MAROUN (Fri Mar 25 2016 - 09:01:46 CDT)
Re: Opinions on Haptic Feedback Devices with NAMD/VMD Axel Kohlmeyer (Fri Mar 25 2016 - 08:52:33 CDT)
Opinions on Haptic Feedback Devices with NAMD/VMD Ben Fritch (Fri Mar 25 2016 - 08:37:31 CDT)
Re: varying two colvar distances simultaneously Giacomo Fiorin (Thu Mar 24 2016 - 16:53:46 CDT)
varying two colvar distances simultaneously Chitrak Gupta (Thu Mar 24 2016 - 16:49:06 CDT)
Opinions on Haptic Feedback Devices with NAMD/VMD Ben Fritch (Thu Mar 24 2016 - 14:29:02 CDT)
force units conversion Olya Kravchenko (Thu Mar 24 2016 - 14:15:05 CDT)
Re: dynamic_cast & runtime type information Ã‰ric Germaneau (Wed Mar 23 2016 - 19:43:44 CDT)
Restarting ABF Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Tue Mar 22 2016 - 13:45:51 CDT)
instantaneous pressure and temp change for multiple run calls? Radak, Brian K (Tue Mar 22 2016 - 13:21:53 CDT)
Parameterizing residues of a polymer faride badalkhani (Tue Mar 22 2016 - 12:47:57 CDT)
Parameterizing residues of a polymer faride badalkhani (Tue Mar 22 2016 - 09:17:46 CDT)
Re: GPU configuration suggestions daniel aguayo (Tue Mar 22 2016 - 06:59:16 CDT)
AW: GPU configuration suggestions Norman Geist (Tue Mar 22 2016 - 05:20:52 CDT)
Re: GPU configuration suggestions Nikhil Maroli (Tue Mar 22 2016 - 04:31:33 CDT)
AW: GPU configuration suggestions Norman Geist (Tue Mar 22 2016 - 04:26:39 CDT)
AW: GPU configuration suggestions Norman Geist (Tue Mar 22 2016 - 03:44:44 CDT)
AW: GPU configuration suggestions Norman Geist (Tue Mar 22 2016 - 02:28:40 CDT)
GPU configuration suggestions Nikhil Maroli (Tue Mar 22 2016 - 00:52:25 CDT)
Re: AW: AW: Testing NAMD scalability Ã‰ric Germaneau (Mon Mar 21 2016 - 22:20:54 CDT)
Postdoctoral opening in biomolecular modeling at IBM Payel Das (Mon Mar 21 2016 - 16:38:19 CDT)
Re: Basic validation of CGenFF Peter Freddolino (Mon Mar 21 2016 - 08:19:53 CDT)
Basic validation of CGenFF faride badalkhani (Mon Mar 21 2016 - 07:31:05 CDT)
AW: AW: Testing NAMD scalability Norman Geist (Mon Mar 21 2016 - 03:31:30 CDT)
Re: AW: Testing NAMD scalability Eric Germaneau (Mon Mar 21 2016 - 03:15:06 CDT)
AW: Testing NAMD scalability Norman Geist (Mon Mar 21 2016 - 02:45:31 CDT)
Testing NAMD scalability Ã‰ric Germaneau (Fri Mar 18 2016 - 20:31:31 CDT)
CGENFF validation faride badalkhani (Fri Mar 18 2016 - 15:12:56 CDT)
Manganese force field Taejin Kim (Fri Mar 18 2016 - 14:07:35 CDT)
Re: charge group faride badalkhani (Fri Mar 18 2016 - 13:36:14 CDT)
dynamic_cast & runtime type information Ã‰ric Germaneau (Fri Mar 18 2016 - 11:46:10 CDT)
Re: charge group Josh Vermaas (Fri Mar 18 2016 - 11:36:21 CDT)
Re: charge group faride badalkhani (Fri Mar 18 2016 - 11:23:39 CDT)
Re: charge group Josh Vermaas (Fri Mar 18 2016 - 11:10:51 CDT)
charge group faride badalkhani (Fri Mar 18 2016 - 10:56:42 CDT)
Fwd: Appropriate FF for a specific solvent faride badalkhani (Fri Mar 18 2016 - 10:53:15 CDT)
Re: ------------- Processor 0 Exiting: Called CmiAbort ------------ Pardis Tabaee (Thu Mar 17 2016 - 12:09:43 CDT)
adaptive biasing force with RMSD colvar Haleh a (Thu Mar 17 2016 - 11:39:45 CDT)
Appropriate FF for a specific solvent faride badalkhani (Thu Mar 17 2016 - 10:48:57 CDT)
2016 ISQBP Meeting: early registration / abstract submission deadline approaching Vlad Cojocaru (Thu Mar 17 2016 - 03:49:47 CDT)
NAMD 2.11 CUDA freezes on windows 8 Ajasja LjubetiÄ (Wed Mar 16 2016 - 13:08:59 CDT)
RE: AW: Tcl script for simulated tempering? Radak, Brian K (Wed Mar 16 2016 - 10:17:07 CDT)
AW: AW: Tcl script for simulated tempering? Norman Geist (Wed Mar 16 2016 - 05:10:14 CDT)
Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Tue Mar 15 2016 - 15:50:18 CDT)
Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Tue Mar 15 2016 - 14:48:58 CDT)
NAMD survey starting Jim Phillips (Tue Mar 15 2016 - 13:34:00 CDT)
RE: AW: Tcl script for simulated tempering? Radak, Brian K (Tue Mar 15 2016 - 13:01:56 CDT)
AW: AW: Tcl script for simulated tempering? Norman Geist (Tue Mar 15 2016 - 10:21:11 CDT)
Re: AW: Tcl script for simulated tempering? Brian Radak (Tue Mar 15 2016 - 08:14:11 CDT)
AW: Tcl script for simulated tempering? Norman Geist (Tue Mar 15 2016 - 02:53:21 CDT)
Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Mon Mar 14 2016 - 11:24:35 CDT)
Re: Fwd: Urey-Bradley parameters Brian Radak (Mon Mar 14 2016 - 10:25:22 CDT)
restarting simulation Francesco Pietra (Mon Mar 14 2016 - 09:45:44 CDT)
Fwd: Urey-Bradley parameters faride badalkhani (Mon Mar 14 2016 - 07:20:08 CDT)
WG: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 Greipel.Joachim_at_mh-hannover.de (Mon Mar 14 2016 - 04:47:28 CDT)
Fwd: ISQBP 2016 meeting - registration opened! Vlad Cojocaru (Mon Mar 14 2016 - 03:13:10 CDT)
Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Fri Mar 11 2016 - 21:42:23 CST)
Tcl script for simulated tempering? Radak, Brian K (Fri Mar 11 2016 - 16:12:21 CST)
Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Fri Mar 11 2016 - 15:31:50 CST)
Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Fri Mar 11 2016 - 14:57:55 CST)
Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Fri Mar 11 2016 - 14:39:06 CST)
Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Fri Mar 11 2016 - 14:34:35 CST)
Re: AW: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 Jim Phillips (Fri Mar 11 2016 - 09:45:19 CST)
Re: Tutorial example of replica exchange Dr. Eddie (Fri Mar 11 2016 - 09:35:03 CST)
Re: AW: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 Josh Vermaas (Fri Mar 11 2016 - 09:29:09 CST)
AW: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 Greipel.Joachim_at_mh-hannover.de (Fri Mar 11 2016 - 01:47:27 CST)
Urey-Bradley parameters faride badalkhani (Fri Mar 11 2016 - 09:10:39 CST)
Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Thu Mar 10 2016 - 20:01:12 CST)
Re: problem with bringing down the pressure Josh Vermaas (Thu Mar 10 2016 - 19:26:12 CST)
AW: Tutorial example of replica exchange Norman Geist (Thu Mar 10 2016 - 16:53:22 CST)
AW: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 Norman Geist (Thu Mar 10 2016 - 16:43:55 CST)
Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Thu Mar 10 2016 - 15:58:45 CST)
Re: Tutorial example of replica exchange Dr. Eddie (Thu Mar 10 2016 - 12:26:19 CST)
problem with bringing down the pressure faride badalkhani (Thu Mar 10 2016 - 11:31:36 CST)
Re: installing NAMD 2.11 Chitrak Gupta (Thu Mar 10 2016 - 11:30:44 CST)
Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Thu Mar 10 2016 - 11:21:00 CST)
Re: Tutorial example of replica exchange Josh Vermaas (Thu Mar 10 2016 - 10:04:07 CST)
Re: Tutorial example of replica exchange Dr. Eddie (Thu Mar 10 2016 - 09:46:50 CST)
AW: Tutorial example of replica exchange Norman Geist (Thu Mar 10 2016 - 02:03:38 CST)
AW: periodic boundary condition in XY, hard wall in Z - errors Norman Geist (Thu Mar 10 2016 - 01:05:33 CST)
periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Wed Mar 09 2016 - 21:23:05 CST)
equilibration error faride badalkhani (Wed Mar 09 2016 - 15:22:25 CST)
Hands-On Workshop on Computational Biophysics: June 6-10 in Pittsburgh, PA Jodi Ann Hadden (Wed Mar 09 2016 - 14:34:10 CST)
NAMD Developer Workshop: May 26-27 in Chicago, IL Jodi Ann Hadden (Wed Mar 09 2016 - 14:31:56 CST)
cellBasisVectors faride badalkhani (Wed Mar 09 2016 - 10:27:53 CST)
Re: installing NAMD 2.11 faride badalkhani (Wed Mar 09 2016 - 07:54:23 CST)
Re: installing NAMD 2.11 Ajasja LjubetiÄ (Wed Mar 09 2016 - 07:38:39 CST)
installing NAMD 2.11 faride badalkhani (Wed Mar 09 2016 - 07:32:46 CST)
Tutorial example of replica exchange Dr. Eddie (Tue Mar 08 2016 - 16:55:34 CST)
AW: selection error in forces script Norman Geist (Tue Mar 08 2016 - 01:35:26 CST)
Re: selection error in forces script Olya Kravchenko (Tue Mar 08 2016 - 00:08:00 CST)
selection error in forces script Olya Kravchenko (Mon Mar 07 2016 - 23:02:34 CST)
Re: segmentation error Giacomo Fiorin (Fri Mar 04 2016 - 10:54:29 CST)
segmentation error Stefano Guglielmo (Fri Mar 04 2016 - 04:15:01 CST)
AW: applying constant force only within certain part of simulation cell? Norman Geist (Fri Mar 04 2016 - 02:27:49 CST)
Re: applying constant force only within certain part of simulation cell? Ajasja LjubetiÄ (Thu Mar 03 2016 - 15:27:35 CST)
applying constant force only within certain part of simulation cell? Olya Kravchenko (Thu Mar 03 2016 - 14:00:33 CST)
Re: æ¥è‡ª"ZOU Changling" <zoucl@ihep.ac.cn>çš„é‚®ä»¶ Jeff Comer (Thu Mar 03 2016 - 11:22:49 CST)
Constraint failure in RATTLE algorithm Stefano Guglielmo (Tue Mar 01 2016 - 19:18:05 CST)
Re: INTERNAL COORDINATES Josh Vermaas (Tue Mar 01 2016 - 08:28:33 CST)
INTERNAL COORDINATES faride badalkhani (Tue Mar 01 2016 - 07:52:09 CST)
Combination of top_all36_cgenff with top_all36_prot faride badalkhani (Mon Feb 29 2016 - 15:03:31 CST)
Re: Energy gradient in colvars.state file Giacomo Fiorin (Mon Feb 29 2016 - 14:25:35 CST)
Energy gradient in colvars.state file Carlo Guardiani (Mon Feb 29 2016 - 13:09:31 CST)
Q=B4=D7=D4"ZOU_Changling"_<zoucl@ihep.ac.cn>=B5=C4=D3=CA=BC=FE?= ZOU Changling (Mon Feb 29 2016 - 02:43:31 CST)
AW: problem in running targeted MD Norman Geist (Mon Feb 29 2016 - 01:37:21 CST)
Re: AW: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓÊ¼þ ZOU Changling (Sun Feb 28 2016 - 19:36:06 CST)
plumed Stefano Guglielmo (Sun Feb 28 2016 - 10:21:32 CST)
AW: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓÊ¼þ Norman Geist (Fri Feb 26 2016 - 06:10:11 CST)
Q=B4=D7=D4"ZOU_Changling"_<zoucl@ihep.ac.cn>=B5=C4=D3=CA=BC=FE?= ZOU Changling (Fri Feb 26 2016 - 05:20:03 CST)
AW: problem in running targeted MD Norman Geist (Fri Feb 26 2016 - 01:57:15 CST)
test area method to calculate surface tension Yan Shen (Thu Feb 25 2016 - 15:05:45 CST)
AW: problem in running targeted MD Norman Geist (Thu Feb 25 2016 - 01:38:33 CST)
problem in running targeted MD giulia palermo (Wed Feb 24 2016 - 19:56:11 CST)
AW: Energy increase with fixed atoms in POPC membrane Norman Geist (Mon Feb 22 2016 - 02:04:39 CST)
Re: Energy increase with fixed atoms in POPC membrane Tristan Croll (Fri Feb 19 2016 - 10:51:52 CST)
AW: Energy increase with fixed atoms in POPC membrane Norman Geist (Fri Feb 19 2016 - 01:47:51 CST)
Re: external HPC resource Mahya Hemmat (Thu Feb 18 2016 - 17:10:12 CST)
Re: Should you cap C and N termini? Gianluca Interlandi (Thu Feb 18 2016 - 12:57:24 CST)
external HPC resource Deng, Jinxia (Nancy) (Thu Feb 18 2016 - 10:23:36 CST)
Re: Should you cap C and N termini? Vlad Cojocaru (Thu Feb 18 2016 - 09:31:56 CST)
Should you cap C and N termini? ashika torikora (Thu Feb 18 2016 - 07:09:10 CST)
AW: Energy increase with fixed atoms in POPC membrane Norman Geist (Thu Feb 18 2016 - 02:03:09 CST)
Energy increase with fixed atoms in POPC membrane Mihaela Drenscko (Wed Feb 17 2016 - 16:27:15 CST)
Re: Replica Exchange US, Colvar suggestion Laurent Chaloin (Sat Feb 13 2016 - 02:02:24 CST)
Re: Replica Exchange US, Colvar suggestion Laurent Chaloin (Sat Feb 13 2016 - 01:53:46 CST)
AW: vmd-l: moving atoms and updating distances Norman Geist (Mon Feb 15 2016 - 00:11:47 CST)
Re: Replica Exchange US, Colvar suggestion Abhishek TYAGI (Sat Feb 13 2016 - 22:39:29 CST)
Re: Replica Exchange US, Colvar suggestion Giacomo Fiorin (Sat Feb 13 2016 - 13:21:00 CST)
Replica Exchange US, Colvar suggestion Abhishek TYAGI (Sat Feb 13 2016 - 01:07:38 CST)
Re: Non respect of sequence of commands in command file Josh Vermaas (Fri Feb 12 2016 - 11:04:28 CST)
Non respect of sequence of commands in command file R. Charbel MAROUN (Fri Feb 12 2016 - 05:11:39 CST)
Re: velocity computation Tristan Croll (Tue Feb 09 2016 - 03:04:40 CST)
AW: velocity computation Norman Geist (Tue Feb 09 2016 - 02:22:54 CST)
Re: velocity computation Tristan Croll (Mon Feb 08 2016 - 12:33:16 CST)
Re: velocity computation 'Patrick Welche' (Mon Feb 08 2016 - 08:34:19 CST)
AW: velocity computation Norman Geist (Mon Feb 08 2016 - 00:51:46 CST)
velocity computation Patrick Welche (Fri Feb 05 2016 - 13:05:25 CST)
Fwd: namd on Windows 10 Branko (Fri Feb 05 2016 - 08:13:51 CST)
Re: namd on Windows 10 Kostas Malavazos (Thu Feb 04 2016 - 14:14:09 CST)
namd on Windows 10 Branko (Thu Feb 04 2016 - 12:24:14 CST)
About parseFEP error Atsutoshi Okabe (Wed Feb 03 2016 - 08:01:21 CST)
bond energy high Ipsita Basu (Wed Feb 03 2016 - 05:15:35 CST)
NAMD Implicit GB Parameters Samuel Bowerman (Mon Feb 01 2016 - 12:41:03 CST)
Re: PBC in lipid bilayer: receptor vs. ligand R. Charbel MAROUN (Mon Feb 01 2016 - 10:39:06 CST)
AW: Re: tclBC relective boundaries Norman Geist (Mon Feb 01 2016 - 00:10:45 CST)
Re: Lennard-Jones potential in coarse grained MD Yongcheng Zhou (Sun Jan 31 2016 - 00:16:37 CST)
Re: Problems in NAMD's code about real implementation of function named ComputeNonbondedUtil:calc_pair_energy Peter Freddolino (Sat Jan 30 2016 - 21:00:17 CST)
Re: Lennard-Jones potential in coarse grained MD bay__gulf618_at_sina.com (Sat Jan 30 2016 - 01:19:17 CST)
Lennard-Jones potential in coarse grained MD Yongcheng Zhou (Sat Jan 30 2016 - 00:36:20 CST)
Re: tclBC relective boundaries Art (Fri Jan 29 2016 - 17:27:02 CST)
Problems in NAMD's code about real implementation of function named ComputeNonbondedUtil:calc_pair_energy yeguoqiao (Fri Jan 29 2016 - 09:05:31 CST)
tclBC relective boundaries Art (Fri Jan 29 2016 - 13:51:17 CST)
MD trajectory analysis Deng, Jinxia (Nancy) (Thu Jan 28 2016 - 13:02:14 CST)
Re: PBC in lipid bilayer: receptor vs. ligand Jeff Comer (Thu Jan 28 2016 - 12:38:45 CST)
Re: PBC in lipid bilayer: receptor vs. ligand R. Charbel MAROUN (Thu Jan 28 2016 - 11:59:14 CST)
Re: PBC in lipid bilayer: receptor vs. ligand Josh Vermaas (Thu Jan 28 2016 - 11:09:08 CST)
Re: PBC in lipid bilayer: receptor vs. ligand R. Charbel MAROUN (Thu Jan 28 2016 - 11:03:17 CST)
Re: PBC in lipid bilayer: receptor vs. ligand Josh Vermaas (Thu Jan 28 2016 - 09:43:21 CST)
Re: PBC in lipid bilayer: receptor vs. ligand R. Charbel MAROUN (Thu Jan 28 2016 - 05:26:33 CST)
AW: PBC in lipid bilayer: receptor vs. ligand Norman Geist (Wed Jan 27 2016 - 09:35:05 CST)
Re: PBC in lipid bilayer: receptor vs. ligand Josh Vermaas (Wed Jan 27 2016 - 09:22:40 CST)
Re: PBC in lipid bilayer: receptor vs. ligand Ajasja LjubetiÄ (Wed Jan 27 2016 - 09:21:11 CST)
PBC in lipid bilayer: receptor vs. ligand R. Charbel MAROUN (Wed Jan 27 2016 - 07:54:34 CST)
Re: calculating replica exchange acceptance ratio Chitrak Gupta (Wed Jan 27 2016 - 04:18:38 CST)
Re: Ajasja LjubetiÄ (Wed Jan 27 2016 - 03:39:04 CST)
(no subject) Srijita Paul (Tue Jan 26 2016 - 23:06:12 CST)
(no subject) Srijita Paul (Tue Jan 26 2016 - 23:02:28 CST)
AW: calculating replica exchange acceptance ratio Norman Geist (Tue Jan 26 2016 - 08:03:40 CST)
Re: segmentation fault in ABF simulations Azadeh Alavi (Mon Jan 25 2016 - 12:31:10 CST)
Re: segmentation fault in ABF simulations Azadeh Alavi (Mon Jan 25 2016 - 12:11:58 CST)
Re: segmentation fault in ABF simulations Azadeh Alavi (Mon Jan 25 2016 - 11:00:26 CST)
Re: calculating replica exchange acceptance ratio Chitrak Gupta (Mon Jan 25 2016 - 09:58:31 CST)
Re: compute capability Josh Vermaas (Mon Jan 25 2016 - 09:52:37 CST)
Re: calculating replica exchange acceptance ratio Chitrak Gupta (Mon Jan 25 2016 - 09:51:48 CST)
segmentation fault in ABF simulations Azadeh Alavi (Mon Jan 25 2016 - 07:58:49 CST)
AW: calculating replica exchange acceptance ratio Norman Geist (Mon Jan 25 2016 - 05:51:31 CST)
AW: calculating replica exchange acceptance ratio Norman Geist (Mon Jan 25 2016 - 04:37:56 CST)
Re: calculating replica exchange acceptance ratio Chitrak Gupta (Mon Jan 25 2016 - 02:54:15 CST)
AW: PBC BUG in coorfile + pair interaction Norman Geist (Mon Jan 25 2016 - 02:33:18 CST)
Re: Enabling GPU for Replica exchange umbrella sampling Abhishek TYAGI (Mon Jan 25 2016 - 01:49:23 CST)
AW: calculating replica exchange acceptance ratio Norman Geist (Mon Jan 25 2016 - 01:13:51 CST)
AW: Enabling GPU for Replica exchange umbrella sampling Norman Geist (Mon Jan 25 2016 - 01:06:05 CST)
calculating replica exchange acceptance ratio Chitrak Gupta (Sun Jan 24 2016 - 23:16:09 CST)
compute capability Stefano Guglielmo (Sun Jan 24 2016 - 17:15:43 CST)
Re: Enabling GPU for Replica exchange umbrella sampling Abhishek TYAGI (Sat Jan 23 2016 - 13:05:26 CST)
AW: Enabling GPU for Replica exchange umbrella sampling Norman Geist (Fri Jan 22 2016 - 03:09:24 CST)
AW: Re: Enabling GPU for Replica exchange umbrella sampling Norman Geist (Fri Jan 22 2016 - 03:07:59 CST)
charmc rpath Scott Brozell (Thu Jan 21 2016 - 22:04:41 CST)
Re: Enabling GPU for Replica exchange umbrella sampling Abhishek TYAGI (Thu Jan 21 2016 - 22:02:59 CST)
Re: multipld .dcd analysis by VMD Zhao Qin (Thu Jan 21 2016 - 12:40:25 CST)
AW: PBC BUG in coorfile + pair interaction Norman Geist (Thu Jan 21 2016 - 04:32:33 CST)
PBC BUG in coorfile + pair interaction Norman Geist (Thu Jan 21 2016 - 03:50:59 CST)
Enabling GPU for REUS Abhishek TYAGI (Wed Jan 20 2016 - 21:12:50 CST)
multipld .dcd analysis by VMD Deng, Jinxia (Nancy) (Wed Jan 20 2016 - 13:53:21 CST)
Re: LSU SuperMIC Kenneth Huang (Tue Jan 19 2016 - 17:15:39 CST)
LSU SuperMIC Jeff Comer (Tue Jan 19 2016 - 16:21:39 CST)
Re: Replica Exchange Jason Swails (Tue Jan 19 2016 - 15:06:24 CST)
Re: Replica Exchange Chitrak Gupta (Tue Jan 19 2016 - 14:40:20 CST)
Replica Exchange Dr. Eddie (Tue Jan 19 2016 - 10:35:00 CST)
»Ø¸´: about User-Defined Forces bay__gulf618_at_sina.com (Mon Jan 18 2016 - 05:23:00 CST)
about User-Defined Forces ¸ß¾ü (Mon Jan 18 2016 - 03:28:31 CST)
RE: RE: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Tim.Ho_at_csiro.au (Thu Jan 14 2016 - 22:02:44 CST)
Recover the PMF along an unbiased CV Felipe Merino (Thu Jan 14 2016 - 16:11:37 CST)
RE: [Non-DoD Source] RE: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Tim.Ho_at_csiro.au (Thu Jan 14 2016 - 16:00:28 CST)
RE: [Non-DoD Source] RE: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Thu Jan 14 2016 - 09:24:50 CST)
RE: Compilation error across Intel 14,15 and 16 (UNCLASSIFIED) Tim.Ho_at_csiro.au (Wed Jan 13 2016 - 22:28:53 CST)
2.11 how to remove charmrun remote-shell options Scott Brozell (Wed Jan 13 2016 - 12:04:54 CST)
AW: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Norman Geist (Wed Jan 13 2016 - 02:17:01 CST)
restart namd calculations Bylund, Tatsiana (NIH/NIAID) [F] (Tue Jan 12 2016 - 16:55:09 CST)
Re: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Brunner, Robert Kraemer (Tue Jan 12 2016 - 14:31:36 CST)
RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 14:04:36 CST)
AW: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Norman Geist (Tue Jan 12 2016 - 13:23:21 CST)
RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 09:44:54 CST)
Re: Aoid protein to reach periodic boundary Jeff Comer (Tue Jan 12 2016 - 09:30:36 CST)
AW: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Norman Geist (Tue Jan 12 2016 - 08:31:52 CST)
RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 07:27:59 CST)
Re: Aoid protein to reach periodic boundary Felipe Merino (Tue Jan 12 2016 - 06:13:43 CST)
Re: Aoid protein to reach periodic boundary Branko (Tue Jan 12 2016 - 05:41:21 CST)
AW: Compilation error across Intel 14,15 and 16 (UNCLASSIFIED) Norman Geist (Tue Jan 12 2016 - 02:16:38 CST)
Aoid protein to reach periodic boundary Dharmeshkumar Patel (Mon Jan 11 2016 - 18:15:16 CST)
Compilation error across Intel 14,15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Mon Jan 11 2016 - 13:10:19 CST)
Re: Regarding system forces in NAMD sruthi c k (Fri Jan 08 2016 - 06:14:08 CST)
Fwd: Regarding system forces in NAMD sruthi c k (Fri Jan 08 2016 - 03:38:26 CST)
Re: TIP4P/2005 par file by Jordi Faraudo Monika Madhavi (Sat Jan 09 2016 - 14:38:50 CST)
Re: TIP4P/2005 par file by Jordi Faraudo Fotis Baltoumas (Sat Jan 09 2016 - 12:13:01 CST)
TIP4P/2005 par file by Jordi Faraudo Monika Madhavi (Sat Jan 09 2016 - 07:16:17 CST)
Re: Regarding system forces in NAMD Giacomo Fiorin (Fri Jan 08 2016 - 08:36:45 CST)
PhD and postdoctoral positions in biomolecular simulation Allison, Jane (Thu Jan 07 2016 - 19:01:29 CST)
Re: Regarding system forces in NAMD sruthi c k (Thu Jan 07 2016 - 11:43:49 CST)
Re: Regarding system forces in NAMD Giacomo Fiorin (Thu Jan 07 2016 - 09:18:35 CST)
Re: Regarding system forces in NAMD Giacomo Fiorin (Thu Jan 07 2016 - 09:14:45 CST)
Re: Regarding system forces in NAMD sruthi c k (Thu Jan 07 2016 - 09:13:57 CST)
Re: Regarding system forces in NAMD Giacomo Fiorin (Thu Jan 07 2016 - 09:10:39 CST)
Regarding system forces in NAMD sruthi c k (Thu Jan 07 2016 - 06:49:51 CST)
Re: Regarding merging of .grad files obtained from ABF simulations sruthi c k (Thu Jan 07 2016 - 04:31:11 CST)
Re: Regarding merging of .grad files obtained from ABF simulations JÃ©rÃ´me HÃ©nin (Thu Jan 07 2016 - 04:07:17 CST)
Regarding merging of .grad files obtained from ABF simulations sruthi c k (Thu Jan 07 2016 - 01:49:18 CST)
(no subject) Srijita Paul (Wed Jan 06 2016 - 22:25:56 CST)
Re: solvent other than water Jeff Comer (Wed Jan 06 2016 - 13:39:14 CST)
solvent other than water Deng, Jinxia (Nancy) (Wed Jan 06 2016 - 12:17:11 CST)
Re: NAMD 2.11 released Jeff Comer (Wed Jan 06 2016 - 08:35:12 CST)
Re: NAMD 2.11 released JC Gumbart (Tue Jan 05 2016 - 16:16:03 CST)
Equilibration fails for long time ,NPT Nikhil Maroli (Sun Jan 03 2016 - 11:42:32 CST)
GBIS error sunyeping (Sat Jan 02 2016 - 22:55:10 CST)

Last message date: Sat Dec 30 2017 - 12:48:03 CST
Archived on: Sun Dec 31 2017 - 23:21:52 CST

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