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About this archive
Starting: Sat Jan 02 2016 - 22:55:30 CST
Ending: Sat Dec 30 2017 - 12:48:03 CST
- question about point substitution A→U parinaz bashirbanaem (Sat Dec 30 2017 - 12:47:43 CST)
- (no subject) Suresh Ghimire (Fri Dec 29 2017 - 19:57:56 CST)
- Having problem with restarting colvar distance, Aliasghar Alizadeh-Mojarad (Fri Dec 29 2017 - 02:10:07 CST)
- Gradual cooling of the system Monika Madhavi (Sun Dec 24 2017 - 22:27:27 CST)
- [NAMD] Question about patches The Cromicus Productions (Sun Dec 24 2017 - 03:49:07 CST)
- Re: [NAMD] Question about patches JC Gumbart (Sun Dec 24 2017 - 15:16:10 CST)
- RE: [NAMD] Question about patches Lennart Nilsson (Mon Dec 25 2017 - 09:17:51 CST)
- Re: [NAMD] Question about patches The Cromicus Productions (Mon Dec 25 2017 - 17:29:06 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 - 18:04:43 CST)
- RE: [NAMD] Question about patches Lennart Nilsson (Tue Dec 26 2017 - 04:43:30 CST)
- Re: [NAMD] Question about patches JC Gumbart (Tue Dec 26 2017 - 09:26:12 CST)
- Re: [NAMD] Question about patches The Cromicus Productions (Mon Dec 25 2017 - 17:29:06 CST)
- (no subject) Suresh Ghimire (Fri Dec 22 2017 - 09:54:23 CST)
- facing problem while downloading NAMD Jyoti Sharma (Fri Dec 22 2017 - 03:20:26 CST)
- gbsa Stefano Guglielmo (Tue Dec 19 2017 - 19:55:21 CST)
- reconstructing pmf Stefano Guglielmo (Mon Dec 18 2017 - 18:24:15 CST)
- Re: reconstructing pmf Vermaas, Joshua (Mon Dec 18 2017 - 18:35:31 CST)
- Re: reconstructing pmf Giacomo Fiorin (Mon Dec 18 2017 - 19:40:03 CST)
- Re: reconstructing pmf Stefano Guglielmo (Tue Dec 19 2017 - 02:48:53 CST)
- Re: reconstructing pmf Giacomo Fiorin (Tue Dec 19 2017 - 08:08:03 CST)
- Re: reconstructing pmf Jeff Comer (Tue Dec 19 2017 - 09:20:57 CST)
- Re: reconstructing pmf Giacomo Fiorin (Tue Dec 19 2017 - 10:27:09 CST)
- Re: reconstructing pmf Jeff Comer (Tue Dec 19 2017 - 12:52:21 CST)
- Re: reconstructing pmf Stefano Guglielmo (Tue Dec 19 2017 - 18:17:35 CST)
- Re: reconstructing pmf Giacomo Fiorin (Tue Dec 19 2017 - 18:24:46 CST)
- Re: reconstructing pmf Stefano Guglielmo (Wed Dec 20 2017 - 01:55:15 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)
- tcl used for binary compilation Francesco Pietra (Mon Dec 18 2017 - 14:26:30 CST)
- colvars: Error: keyword "translatereference" is not supported, or not recognized in this context. Victor Kwan (Sun Dec 17 2017 - 22:35:33 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)
- Define a colvar from other colvars Ben Adams (Thu Dec 14 2017 - 13:50:29 CST)
- Script for Terachem QMMM Chris Butch (Thu Dec 14 2017 - 03:29:17 CST)
- Periodic molecules in NAMD Bogdan MAREKHA (Wed Dec 13 2017 - 05:13:54 CST)
- Re: namd-l digest V1 #2316 Yaxin An (Fri Dec 08 2017 - 09:06:19 CST)
- atom selection error Shahee Islam (Fri Dec 08 2017 - 02:33:19 CST)
- Re: atom selection error Peter Freddolino (Fri Dec 08 2017 - 07:59:51 CST)
- Re: atom selection error Shahee Islam (Fri Dec 08 2017 - 08:22:51 CST)
- Re: atom selection error Brian Radak (Fri Dec 08 2017 - 10:41:57 CST)
- Re: atom selection error Peter Freddolino (Fri Dec 08 2017 - 11:54:00 CST)
- Re: atom selection error Shahee Islam (Mon Dec 11 2017 - 00:04:47 CST)
- Re: atom selection error Peter Freddolino (Mon Dec 11 2017 - 00:24:47 CST)
- Re: atom selection error Brian Radak (Mon Dec 11 2017 - 11:14:36 CST)
- Re: atom selection error Vermaas, Joshua (Mon Dec 11 2017 - 11:28:09 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 - 00:38:19 CST)
- Re: atom selection error Shahee Islam (Mon Dec 11 2017 - 00:52:18 CST)
- Re: atom selection error Atanu Maity (Mon Dec 11 2017 - 08:30:55 CST)
- Re: atom selection error Peter Freddolino (Mon Dec 11 2017 - 14:26:26 CST)
- Re: atom selection error Shahee Islam (Tue Dec 12 2017 - 01:31:22 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)
- metadynamics run in NAMD or using plumed in NAMD Rabeta Yeasmin (Thu Dec 07 2017 - 17:49:22 CST)
- Re: metadynamics run in NAMD or using plumed in NAMD yjcoshc (Thu Dec 07 2017 - 19:22:06 CST)
- Re: metadynamics run in NAMD or using plumed in NAMD Rabeta Yeasmin (Fri Dec 08 2017 - 02:06:22 CST)
- Re: Re: metadynamics run in NAMD or using plumed in NAMD Giacomo Fiorin (Fri Dec 08 2017 - 07:08:36 CST)
- Re: Re: metadynamics run in NAMD or using plumed in NAMD Rabeta Yeasmin (Fri Dec 08 2017 - 12:14:11 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 - 12:39:49 CST)
- Re: Re: metadynamics run in NAMD or using plumed in NAMD Giacomo Fiorin (Fri Dec 08 2017 - 07:08:36 CST)
- Free energy did not converge by using ABF Yaxin An (Thu Dec 07 2017 - 17:22:31 CST)
- nvt vs nve file NEHİR NALINCI (Mon Dec 04 2017 - 12:11:27 CST)
- Colvar Error Souvik Sinha (Mon Dec 04 2017 - 07:33:12 CST)
- colvars/rmsd: Error: definition for atom group "atoms" not found. Victor Kwan (Sun Dec 03 2017 - 05:12:06 CST)
- (no subject) Shahee Islam (Fri Dec 01 2017 - 02:28:17 CST)
- [NAMD] Patch 5MC2 The Cromicus Productions (Wed Nov 29 2017 - 17:45:16 CST)
- Targeted MD, "Biased atoms" and "Fitted atoms", RMSD 黄姝姮 (Wed Nov 29 2017 - 07:27:15 CST)
- Electric field simulation: eFieldNormalized Carlo Guardiani (Tue Nov 28 2017 - 13:53:57 CST)
- nan for Drude's LP in distance-like colvars Bogdan MAREKHA (Fri Nov 24 2017 - 10:44:01 CST)
- SMP instructions for multi-node calculation on POWER 8 + P100 Adrien Cerdan (Wed Nov 22 2017 - 10:09:51 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)
- 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)
- NPT simulations with PLUMED in NAMD Eric Lang (Wed Nov 15 2017 - 07:58:27 CST)
- missing parameters. NEHİR NALINCI (Wed Nov 15 2017 - 06:53:06 CST)
- Change pressure during simulation Monika Madhavi (Wed Nov 15 2017 - 01:07:39 CST)
- NAMD QM/MM Constanza Galaz Araya (Tue Nov 14 2017 - 10:08:45 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)
- About the performance of RAMD Francesco Pietra (Fri Nov 10 2017 - 10:55:42 CST)
- Downloads are .tar files but have .tar.gz extension Toon Verstraelen (Thu Nov 09 2017 - 05:07:26 CST)
- NAMD job termination Amali Guruge (Wed Nov 08 2017 - 21:01:25 CST)
- RMSD colvar not working in NAMD2.12 Linux version Abhaysinh Gaikwad (Tue Nov 07 2017 - 21:46:28 CST)
- Psf file generation with Gromacs Parameters Amali Guruge (Mon Nov 06 2017 - 19:53:58 CST)
- problem in writing the coor files Fidan Sumbul (Mon Nov 06 2017 - 11:11:28 CST)
- Running multiple-replicas metadynamics Prapasiri Pongprayoon (Fri Nov 03 2017 - 18:30:11 CDT)
- Some water molecules are missing in psf Amali Guruge (Thu Nov 02 2017 - 17:33:06 CDT)
- RMSD of backbone changes rapidly at the beginning of production run Monika Madhavi (Thu Nov 02 2017 - 04:52:11 CDT)
- Re: RMSD of backbone changes rapidly at the beginning of production run Peter Freddolino (Thu Nov 02 2017 - 09:02:13 CDT)
- Re: RMSD of backbone changes rapidly at the beginning of production run Fidan Sumbul (Fri Nov 03 2017 - 06:27:42 CDT)
- Which NAMD-Build for my local HPC? Bassam Haddad (Tue Oct 31 2017 - 13:34:12 CDT)
- [NAMD] Too many collective variables? The Cromicus Productions (Thu Oct 26 2017 - 15:11:19 CDT)
- Error on Settle.C when compiling NAMD with Intel Compiler Florian Blanc (Wed Oct 25 2017 - 15:26:57 CDT)
- Re: Error on Settle.C when compiling NAMD with Intel Compiler Victor Ovchinnikov (Wed Oct 25 2017 - 15:59:42 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 Florian Blanc (Thu Oct 26 2017 - 12:34:06 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 Nov 09 2017 - 11:00:09 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 Oct 26 2017 - 12:34:06 CDT)
- Amber force filed input failure on GPU Bata Zsófia (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 Zahra Mohammadi (Wed Oct 25 2017 - 02:58:36 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)
- 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)
- building system with or without water for metadynamics Rabeta Yeasmin (Tue Oct 17 2017 - 16:52:38 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)
- 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)
- REST2 simulations: Corecting shifted dcd files! Bhati, Agastya (Wed Oct 11 2017 - 14:36:14 CDT)
- Implementation of sortreplicas executable for restarted REST2 simulations Bhati, Agastya (Wed Oct 11 2017 - 14:12:44 CDT)
- Re: Implementation of sortreplicas executable for restarted REST2 simulations Chitrak Gupta (Wed Oct 11 2017 - 14:32:54 CDT)
- Re: Implementation of sortreplicas executable for restarted REST2 simulations Bhati, Agastya (Wed Oct 11 2017 - 14:50:46 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 (Thu Oct 12 2017 - 06:50:40 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 - 09:00:27 CDT)
- Re: Implementation of sortreplicas executable for restarted REST2 simulations Bhati, Agastya (Wed Oct 11 2017 - 14:50:46 CDT)
- Re: Implementation of sortreplicas executable for restarted REST2 simulations Chitrak Gupta (Wed Oct 11 2017 - 14:32:54 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)
- Sample umbrella sampling input file Rabeta Yeasmin (Fri Oct 06 2017 - 17:14:02 CDT)
- NAMD on Stampede 2 Chitrak Gupta (Thu Oct 05 2017 - 18:23:05 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)
- Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation Brian Radak (Thu Oct 05 2017 - 15:30:28 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: 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 - 14:19:56 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 - 14:04:39 CDT)
- Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation Brian Radak (Thu Oct 05 2017 - 15:30:28 CDT)
- Constrain on DNA when using ABF for protein-DNA system Mehdi Bagherpour (Thu Oct 05 2017 - 13:25:33 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)
- ion moving laterally during Umbrella Sampling? Olya Kravchenko (Tue Oct 03 2017 - 12:45:09 CDT)
- colvars: keepFreeEnergyFiles doesn't work in latest colvars version yjcoshc (Fri Sep 29 2017 - 21:38:13 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)
- Building namd 2.12 from source an ARM64 architecture istamkos_at_auth.gr (Wed Sep 27 2017 - 17:06:00 CDT)
- Re: Building namd 2.12 from source an ARM64 architecture Vermaas, Joshua (Wed Sep 27 2017 - 18:09:31 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 istamkos_at_auth.gr (Fri Sep 29 2017 - 17:38:21 CDT)
- margin and pressure in CUDA version JC Gumbart (Wed Sep 27 2017 - 11:48:52 CDT)
- minimum CUDA compute capability required for NAMD2.12 Albers, Thomas (Sat Sep 23 2017 - 16:03:24 CDT)
- How to sample pressure from NAMD log file. Daipayan Sarkar (Thu Sep 21 2017 - 22:16:54 CDT)
- displacement of protein Estefanía Hugo (Thu Sep 21 2017 - 09:08:19 CDT)
- Build NAMD with CUDA for unix workstation (centos 7) Daipayan Sarkar (Wed Sep 20 2017 - 01:54:25 CDT)
- FAD parameter and topology files amit kumar (Tue Sep 19 2017 - 23:12:39 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: 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)
- 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 - 11:39:05 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? 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? 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? Jérôme Hénin (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 - 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)
- 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)
- 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)
- 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)
- Molecule-based Electrostatics Cutoff? David Huggins (Mon Sep 11 2017 - 16:58:59 CDT)
- extracting avarage pdb from dcd file Srijita Paul (Mon Sep 11 2017 - 00:48:06 CDT)
- minimization error Natasha Gupta (Fri Sep 08 2017 - 19:48:14 CDT)
- The number of QM atoms received is different than expected Haohao Fu (Fri Sep 08 2017 - 04:01:24 CDT)
- Free MD simulation (Production run) Roshan Shrestha (Fri Sep 08 2017 - 02:32:50 CDT)
- -nan values and fatal error Natasha Gupta (Thu Sep 07 2017 - 11:24:29 CDT)
- No minimized system after running minimization in NAMD Roshan Shrestha (Thu Sep 07 2017 - 09:17:02 CDT)
- Concatenating log files Roshan Shrestha (Wed Sep 06 2017 - 11:07:51 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)
- 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: Dihedral colvar Jérôme Hénin (Mon Sep 04 2017 - 07:40:26 CDT)
- Re: Dihedral colvar PRITI ROY (Fri Sep 08 2017 - 08:44:31 CDT)
- Re: Dihedral colvar Jérôme Hénin (Fri Sep 08 2017 - 08:53:28 CDT)
- Re: Dihedral colvar PRITI ROY (Fri Sep 08 2017 - 13:55:01 CDT)
- Re: Dihedral colvar Vermaas, Joshua (Fri Sep 08 2017 - 14:06:25 CDT)
- Re: Dihedral colvar PRITI ROY (Fri Sep 08 2017 - 14:33:45 CDT)
- Re: Dihedral colvar Giacomo Fiorin (Fri Sep 08 2017 - 14:54:44 CDT)
- Re: Dihedral colvar PRITI ROY (Fri Sep 08 2017 - 08:44:31 CDT)
- Re: Dihedral colvar Jérôme Hénin (Mon Sep 04 2017 - 07:40:26 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)
- Constraining and imparting motion to a geometry Abhaysinh Gaikwad (Fri Sep 01 2017 - 14:47:21 CDT)
- AW: NAMD-2.12 CUDA2 and PMECUDA problems Norman Geist (Fri Sep 01 2017 - 03:23:28 CDT)
- Regular vs US sampling runs. jeevan gc (Thu Aug 31 2017 - 18:23:43 CDT)
- Re: Regular vs US sampling runs. Vermaas, Joshua (Thu Aug 31 2017 - 18:56:17 CDT)
- Re: Regular vs US sampling runs. jeevan gc (Thu Aug 31 2017 - 20:13:38 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 (Fri Sep 01 2017 - 11:32:27 CDT)
- Re: Regular vs US sampling runs. Vermaas, Joshua (Fri Sep 01 2017 - 11:53:11 CDT)
- Re: Regular vs US sampling runs. jeevan gc (Fri Sep 01 2017 - 16:32:20 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)
- problem with minimization and calculation of force on a fixed atom Ben Adams (Thu Aug 31 2017 - 17:03:21 CDT)
- Re: problem with minimization and calculation of force on a fixed atom Jérôme Hénin (Thu Aug 31 2017 - 17:36:54 CDT)
- Re: problem with minimization and calculation of force on a fixed atom Ben Adams (Fri Sep 01 2017 - 10:36:21 CDT)
- Re: problem with minimization and calculation of force on a fixed atom Jérôme Hénin (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 - 11:01:49 CDT)
- Re: problem with minimization and calculation of force on a fixed atom Jérôme Hénin (Fri Sep 01 2017 - 11:02:52 CDT)
- Re: problem with minimization and calculation of force on a fixed atom Jérôme Hénin (Fri Sep 01 2017 - 11:23:23 CDT)
- Re: problem with minimization and calculation of force on a fixed atom Ben Adams (Fri Sep 01 2017 - 10:36:21 CDT)
- Re: problem with minimization and calculation of force on a fixed atom Jérôme Hénin (Thu Aug 31 2017 - 17:36:54 CDT)
- Proper combination of langevinHydrogen with rigidbonds Benjamin Rousseau (Thu Aug 31 2017 - 10:31:31 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)
- extracting force on a single atom Ben Adams (Wed Aug 30 2017 - 19:18:49 CDT)
- Re: extracting force on a single atom Jérôme Hénin (Thu Aug 31 2017 - 05:37:13 CDT)
- Re: extracting force on a single atom Ben Adams (Thu Aug 31 2017 - 08:38:05 CDT)
- Re: extracting force on a single atom Jérôme Hénin (Thu Aug 31 2017 - 08:46:28 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 Florian Blanc (Thu Aug 31 2017 - 10:07:59 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 Jérôme Hénin (Thu Aug 31 2017 - 10:25:18 CDT)
- Re: extracting force on a single atom Ben Adams (Thu Aug 31 2017 - 08:38:05 CDT)
- Re: extracting force on a single atom Jérôme Hénin (Thu Aug 31 2017 - 05:37:13 CDT)
- Re: vmd-l: 780Ti and NAMD2 David Hardy (Wed Aug 30 2017 - 10:21:40 CDT)
- Re: NAMD-2.12 CUDA2 and PMECUDA problems Nicholas M. Glykos (Tue Aug 29 2017 - 12:54:40 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)
- NAMD-2.12 CUDA2 and PMECUDA problems Norman Geist (Mon Aug 28 2017 - 05:54:58 CDT)
- Movie in VMD Daipayan Sarkar (Sat Aug 26 2017 - 22:56:24 CDT)
- raising temperature after equiliobration t.shivam_at_iitg.ernet.in (Sat Aug 26 2017 - 02:20:20 CDT)
- NAMD2.9-ERROR: Constraint failure in RATTLE algorithm for atom! 王茜茜 (Fri Aug 25 2017 - 22:47:16 CDT)
- NAMD2.9-ERROR: Constraint failure in RATTLE algorithm for atom! 王茜茜 (Fri Aug 25 2017 - 22:33:43 CDT)
- Steered Molecular Dynamics Abhaysinh Gaikwad (Thu Aug 24 2017 - 13:28:49 CDT)
- Simulating Protein/Membrane interface with pre-equiliibrated lipid bilayer Arthur Vale (Wed Aug 23 2017 - 18:58:59 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)
- Issues about Keep_water_out.tcl acript Vidhya Sankar (Fri Aug 18 2017 - 10:25:55 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)
- 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)
- Creating psf file for ligand Roshan Shrestha (Sat Aug 12 2017 - 09:34:29 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)
- simulation crashing in 2nd stage equilibration t.shivam_at_iitg.ernet.in (Fri Aug 11 2017 - 06:32:32 CDT)
- replica_bias and colvars JC Gumbart (Thu Aug 10 2017 - 12:07:45 CDT)
- Re: replica_bias and colvars Giacomo Fiorin (Thu Aug 10 2017 - 12:51:26 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 - 15:25:35 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 - 21:10:21 CDT)
- Re: replica_bias and colvars JC Gumbart (Sat Aug 12 2017 - 06:49:35 CDT)
- Re: replica_bias and colvars Giacomo Fiorin (Sat Aug 12 2017 - 13:29:48 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)
- difference between .vel and .vel.restart t.shivam_at_iitg.ernet.in (Thu Aug 10 2017 - 04:39:49 CDT)
- value of langevinTemp in case of binvelocities t.shivam_at_iitg.ernet.in (Thu Aug 10 2017 - 02:05:43 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: Software for molecular electrostatic calculations Giacomo Fiorin (Wed Aug 09 2017 - 14:16:54 CDT)
- Re: Software for molecular electrostatic calculations Rabeta Yeasmin (Wed Aug 09 2017 - 16:44:01 CDT)
- Re: Software for molecular electrostatic calculations Giacomo Fiorin (Thu Aug 10 2017 - 08:15:28 CDT)
- Re: Software for molecular electrostatic calculations Rabeta Yeasmin (Thu Aug 10 2017 - 10:31:58 CDT)
- Re: Software for molecular electrostatic calculations David Hardy (Thu Aug 17 2017 - 13:28:19 CDT)
- Re: Software for molecular electrostatic calculations Rabeta Yeasmin (Wed Aug 09 2017 - 16:44:01 CDT)
- Re: Software for molecular electrostatic calculations Giacomo Fiorin (Wed Aug 09 2017 - 14:16:54 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)
- 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)
- difference between constraining,restraining and fixing the atoms t.shivam_at_iitg.ernet.in (Fri Aug 04 2017 - 01:25:23 CDT)
- ABF for dihedrals Albers, Thomas (Thu Aug 03 2017 - 12:48:24 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)
- 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)
- Configuration of new HPC Cluster for NAMD and GROMACS Vogel, Alexander (Mon Jul 31 2017 - 05:36:30 CDT)
- How to calculate free energy to unbias colvars restraint? Victoria Lim (Fri Jul 28 2017 - 18:56:44 CDT)
- PACE CG Model Alexander Adams (Fri Jul 28 2017 - 12:53:24 CDT)
- Running NAMD on Intel OmniPath Maxime Boissonneault (Thu Jul 27 2017 - 13:00:04 CDT)
- Re: Running NAMD on Intel OmniPath Mauro Lapelosa (Thu Jul 27 2017 - 13:06:24 CDT)
- Re: Running NAMD on Intel OmniPath Maxime Boissonneault (Thu Jul 27 2017 - 13:47:54 CDT)
- Re: Running NAMD on Intel OmniPath David Hardy (Thu Jul 27 2017 - 14:18:47 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 - 16:36:47 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 (Fri Jul 28 2017 - 10:29:37 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)
- Does FEP really run on Knights Landing? Francesco Pietra (Thu Jul 27 2017 - 11:44:13 CDT)
- polymer Nehir NALINCI (Thu Jul 27 2017 - 03:02:49 CDT)
- Problems running FEP on Lenovo NextScale KNL Francesco Pietra (Wed Jul 26 2017 - 09:23:19 CDT)
- making glucose chains using charmm36 Mohammad Hassan Khatami (Mon Jul 24 2017 - 13:29:18 CDT)
- I don't have any eabf output file. philippe Bourly (Fri Jul 21 2017 - 13:46:39 CDT)
- Re: I don't have any eabf output file. yjcoshc_at_gmail.com (Tue Jul 25 2017 - 05:06:44 CDT)
- Re: I don't have any eabf output file. philippe Bourly (Tue Jul 25 2017 - 05:20:51 CDT)
- Re: Re: I don't have any eabf output file. Haohao (Tue Jul 25 2017 - 06:14:48 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. philippe Bourly (Tue Jul 25 2017 - 07:23:34 CDT)
- Re: Re: I don't have any eabf output file. fhh2626_at_gmail.com (Wed Jul 26 2017 - 01:47:09 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)
- 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)
- "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)
- Compiling NAMD on stampede 2. Chitrak Gupta (Wed Jul 19 2017 - 17:47:07 CDT)
- Re: Compiling NAMD on stampede 2. Giacomo Fiorin (Wed Jul 19 2017 - 20:14:30 CDT)
- Re: Compiling NAMD on stampede 2. Chitrak Gupta (Thu Jul 20 2017 - 11:09:29 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 - 11:29:37 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 (Fri Jul 21 2017 - 12:20:38 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 (Thu Jul 20 2017 - 11:09:29 CDT)
- Re: Compiling NAMD on stampede 2. Giacomo Fiorin (Wed Jul 19 2017 - 20:14:30 CDT)
- eABF - Fullsamples and windows merging philippe Bourly (Wed Jul 19 2017 - 08:41:56 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)
- "Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL João Ribeiro (Mon Jul 17 2017 - 14:45:43 CDT)
- Error in thermodynamic integration for calculating ligand absolute binding free energy Marawan Hussien (Mon Jul 17 2017 - 11:45:22 CDT)
- Simulation of the mechanical stress in NAMD James Starlight (Mon Jul 17 2017 - 02:55:30 CDT)
- ABF: umbrella_int.awk Francesco Pietra (Thu Jul 13 2017 - 10:32:40 CDT)
- Re: ABF: umbrella_int.awk Jérôme Hénin (Thu Jul 13 2017 - 13:14:33 CDT)
- Re: ABF: umbrella_int.awk Francesco Pietra (Fri Jul 14 2017 - 03:39:48 CDT)
- Re: ABF: umbrella_int.awk Giacomo Fiorin (Fri Jul 14 2017 - 08:20:15 CDT)
- Re: ABF: umbrella_int.awk Giacomo Fiorin (Fri Jul 14 2017 - 08:21:10 CDT)
- Re: ABF: umbrella_int.awk Francesco Pietra (Sat Jul 15 2017 - 03:36:33 CDT)
- Re: ABF: umbrella_int.awk yjcoshc_at_gmail.com (Sat Jul 15 2017 - 07:02:33 CDT)
- Re: ABF: umbrella_int.awk Giacomo Fiorin (Sat Jul 15 2017 - 07:04:13 CDT)
- Re: ABF: umbrella_int.awk Francesco Pietra (Sat Jul 15 2017 - 08:45:00 CDT)
- Re: ABF: umbrella_int.awk Francesco Pietra (Fri Jul 14 2017 - 03:39:48 CDT)
- Re: ABF: umbrella_int.awk Jérôme Hénin (Thu Jul 13 2017 - 13:14:33 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)
- 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)
- Collective variable remains at zero during Umbrella Sampling Hemanth Vemuri (Sun Jul 09 2017 - 23:59:18 CDT)
- Cross-term (CMAP) Faramarz Joodaki (Fri Jul 07 2017 - 18:04:48 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: ABF FEP with multichain receptor Jérôme Hénin (Sat Jul 08 2017 - 05:46:31 CDT)
- Re: ABF FEP with multichain receptor Francesco Pietra (Sat Jul 08 2017 - 11:08:41 CDT)
- Re: ABF FEP with multichain receptor Jérôme Hénin (Sat Jul 08 2017 - 15:07:36 CDT)
- Re: ABF FEP with multichain receptor Francesco Pietra (Sun Jul 09 2017 - 00:44:14 CDT)
- Fwd: ABF FEP with multichain receptor Francesco Pietra (Mon Jul 10 2017 - 05:25:30 CDT)
- Fwd: ABF FEP with multichain receptor Francesco Pietra (Tue Jul 11 2017 - 01:20:12 CDT)
- Re: ABF FEP with multichain receptor Jérôme Hénin (Tue Jul 11 2017 - 08:12:51 CDT)
- Re: ABF FEP with multichain receptor Francesco Pietra (Tue Jul 11 2017 - 11:28:48 CDT)
- Re: ABF FEP with multichain receptor Jérôme Hénin (Tue Jul 11 2017 - 11:52:23 CDT)
- Re: ABF FEP with multichain receptor Francesco Pietra (Sat Jul 08 2017 - 11:08:41 CDT)
- Re: ABF FEP with multichain receptor Jérôme Hénin (Sat Jul 08 2017 - 05:46:31 CDT)
- Lipid_bilayer_area_per_lipid_problem_using_NPT_CharmmForcefield yousef nademi (Thu Jul 06 2017 - 20:49:48 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)
- Periodic cell too small with GPUs, not with pur CPUs Francesco Pietra (Wed Jul 05 2017 - 02:09:14 CDT)
- Re: Periodic cell too small with GPUs, not with pur CPUs Joshua . (Wed Jul 05 2017 - 09:39:40 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 Francesco Pietra (Mon Jul 17 2017 - 09:09:20 CDT)
- Re: Periodic cell too small with GPUs, not with pur CPUs David Hardy (Tue Jul 18 2017 - 17:05:00 CDT)
- Re: Periodic cell too small with GPUs, not with pur CPUs Francesco Pietra (Fri Aug 04 2017 - 06:44:37 CDT)
- Re: Periodic cell too small with GPUs, not with pur CPUs David Hardy (Fri Aug 25 2017 - 14:31:31 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 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 (Sat Aug 26 2017 - 08:11:13 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)
- 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)
- 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)
- enhanced sampling of domain motion, GSAfold Dhiraj Srivastava (Sat Jul 01 2017 - 23:49:00 CDT)
- Simulating SDS molecules Siddharth Girdhar (Fri Jun 30 2017 - 09:11:08 CDT)
- veldcdfile command Laura Joana (Wed Jun 28 2017 - 09:59:45 CDT)
- Re: veldcdfile command Jérôme Hénin (Wed Jun 28 2017 - 11:05:58 CDT)
- Re: veldcdfile command Jérôme Hénin (Wed Jun 28 2017 - 11:41:21 CDT)
- Re: veldcdfile command Laura Joana (Wed Jun 28 2017 - 13:09:28 CDT)
- Re: veldcdfile command Giacomo Fiorin (Wed Jun 28 2017 - 13:36:43 CDT)
- Re: veldcdfile command Laura Joana (Wed Jun 28 2017 - 14:25:35 CDT)
- Re: veldcdfile command Laura Joana (Wed Jun 28 2017 - 14:26:17 CDT)
- Re: veldcdfile command Jérôme Hénin (Thu Jun 29 2017 - 05:12:26 CDT)
- Re: veldcdfile command Jérôme Hénin (Thu Jun 29 2017 - 07:11:45 CDT)
- Re: veldcdfile command Laura Joana (Fri Jun 30 2017 - 07:38:02 CDT)
- Re: veldcdfile command Laura Joana (Mon Jul 03 2017 - 06:13:06 CDT)
- Re: veldcdfile command Jérôme Hénin (Wed Jun 28 2017 - 11:41:21 CDT)
- Re: veldcdfile command Jérôme Hénin (Wed Jun 28 2017 - 11:05:58 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 João Ribeiro (Tue Jun 27 2017 - 13:46:57 CDT)
- Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Sun Jun 25 2017 - 05:56:01 CDT)
- Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Mon Jun 26 2017 - 05:28:49 CDT)
- Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Mon Jun 26 2017 - 11:24:59 CDT)
- Re: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Giacomo Fiorin (Mon Jun 26 2017 - 11:32:58 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 (Wed Jun 28 2017 - 11:35:19 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: Fwd: Atoms too fast/periodic cell too small with ABF protein-ligand Francesco Pietra (Wed Jul 05 2017 - 11:03:05 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 (Thu Jul 06 2017 - 01:15:50 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)
- topology file for the residue CSO Hyun (Fri Jun 23 2017 - 11:43:38 CDT)
- measuring Euler angles and polar angles Francesco Pietra (Thu Jun 22 2017 - 12:01:39 CDT)
- Re: measuring Euler angles and polar angles Giacomo Fiorin (Thu Jun 22 2017 - 12:18:00 CDT)
- Re: measuring Euler angles and polar angles Francesco Pietra (Fri Jun 23 2017 - 09:55:31 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 Jérôme Hénin (Fri Jun 23 2017 - 10:04:46 CDT)
- Re: measuring Euler angles and polar angles Francesco Pietra (Fri Jun 23 2017 - 12:06:18 CDT)
- Fwd: measuring Euler angles and polar angles Francesco Pietra (Sat Jun 24 2017 - 01:22:17 CDT)
- Re: measuring Euler angles and polar angles Francesco Pietra (Fri Jun 23 2017 - 09:55:31 CDT)
- Re: measuring Euler angles and polar angles Giacomo Fiorin (Thu Jun 22 2017 - 12:18:00 CDT)
- Harmonic force Keyword "centers" significance Rabeta Yeasmin (Wed Jun 21 2017 - 17:40:43 CDT)
- Re: run namd cuda with srun. Fırat Yılmaz (Wed Jun 21 2017 - 03:36:09 CDT)
- run namd cuda with srun. Fırat Yılmaz (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)
- 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: Defining custom Colvars to measure pmf with Umbrella Sampling Giacomo Fiorin (Tue Jun 20 2017 - 21:49:26 CDT)
- Re: Defining custom Colvars to measure pmf with Umbrella Sampling Radak, Brian K (Wed Jun 21 2017 - 11:16:49 CDT)
- Simulating Protein Entering membrane Arthur Oliveira Vale (Sun Jun 18 2017 - 20:14:32 CDT)
- GaMD in NAMD Chitrak Gupta (Sat Jun 17 2017 - 15:16:18 CDT)
- Re: GaMD in NAMD Francesco Pietra (Sun Jun 18 2017 - 01:04:59 CDT)
- Re: GaMD in NAMD Chitrak Gupta (Sun Jun 18 2017 - 09:20:11 CDT)
- Re: GaMD in NAMD jeevan gc (Sun Jun 18 2017 - 10:49:40 CDT)
- Re: GaMD in NAMD David Hardy (Sun Jun 18 2017 - 11:02:19 CDT)
- Re: GaMD in NAMD Chitrak Gupta (Sun Jun 18 2017 - 14:57:20 CDT)
- Re: GaMD in NAMD Francesco Pietra (Mon Jun 19 2017 - 00:36:19 CDT)
- Re: GaMD in NAMD Chitrak Gupta (Mon Jun 19 2017 - 08:43:37 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)
- 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 "(" Fırat Yılmaz (Thu Jun 15 2017 - 02:30:12 CDT)
- Reg seeting of periodic boundary condition Vidhya Sankar (Wed Jun 14 2017 - 21:59:27 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)
- How to pull protein-Monomer from DNA using ABF without any force on DNA? Mehdi Bagherpour (Tue Jun 13 2017 - 12:30:29 CDT)
- Questions on implementing new collective variable in colvars. yjcoshc (Mon Jun 12 2017 - 22:14:35 CDT)
- Re: Questions on implementing new collective variable in colvars. Axel Kohlmeyer (Mon Jun 12 2017 - 22:38:48 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. Jérôme Hénin (Tue Jun 13 2017 - 10:32:23 CDT)
- Re: Questions on implementing new collective variable in colvars. yjcoshc (Tue Jun 13 2017 - 20:36:32 CDT)
- Re: Questions on implementing new collective variable in colvars. Jérôme Hénin (Wed Jun 14 2017 - 07:26:16 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)
- FEP with ExtraBonds Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION] (Mon Jun 12 2017 - 15:30:59 CDT)
- Converting x,y,z coordinates to dcd file Kashish Punjani (Sun Jun 11 2017 - 12:44:18 CDT)
- Re: namd-l digest V1 #2196 Rabeta Yeasmin (Fri Jun 09 2017 - 15:40:37 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)
- Colvars wall boundaries for CoordNum Wasut Pornpatcharapong (Thu Jun 08 2017 - 19:27:50 CDT)
- Umbrella Sampling colvar file parameters Rabeta Yeasmin (Thu Jun 08 2017 - 12:20:16 CDT)
- Restraining the mass centre coordinate during Umbrella Sampling Rabeta Yeasmin (Wed Jun 07 2017 - 10:46:57 CDT)
- Restring the coordinate during Umbrella Sampling Rabeta Yeasmin (Tue Jun 06 2017 - 16:13:08 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)
- Center of mass drift M. Wong (Fri Jun 02 2017 - 04:10:50 CDT)
- DNA capping Nicholus Bhattacharjee (Thu Jun 01 2017 - 04:11:48 CDT)
- Problem with running on multiple nodes Karteek Bejagam (Wed May 31 2017 - 11:33:48 CDT)
- Fatal error in the simulation of a water box M. Wong (Wed May 31 2017 - 04:04:38 CDT)
- Segmentation fault error with 'nan' pressure and energy Sadegh Faramarzi Ganjabad (Tue May 30 2017 - 16:17:12 CDT)
- Re: Segmentation fault error with 'nan' pressure and energy Richard Overstreet (Tue May 30 2017 - 16:41:33 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 Sadegh Faramarzi Ganjabad (Thu Jun 01 2017 - 13:05:09 CDT)
- Re: Segmentation fault error with 'nan' pressure and energy Sadegh Faramarzi Ganjabad (Tue Jun 06 2017 - 14:07:24 CDT)
- Re: Re: Segmentation fault error with 'nan' pressure and energy Sadegh Faramarzi Ganjabad (Wed May 31 2017 - 13:37:09 CDT)
- Re: Segmentation fault error with 'nan' pressure and energy Brian Radak (Wed May 31 2017 - 18:24:19 CDT)
- Re: Segmentation fault error with 'nan' pressure and energy Richard Overstreet (Tue May 30 2017 - 16:41:33 CDT)
- NAMD crashes when Multilevel Summation Method (MSM) is on Shadrina Maria (Tue May 30 2017 - 10:12:46 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: Error regarding missing angles between perturbed groups for fep calculation Jeff Comer (Thu May 25 2017 - 16:16:18 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 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] (Fri May 26 2017 - 17:03:36 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] (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)
- Equilibrium Energies Theodora Teddy (Tue May 23 2017 - 11:10:19 CDT)
- psfgen readpsf error with no more explanation Sadegh Faramarzi Ganjabad (Wed May 17 2017 - 15:58:37 CDT)
- Writing pdb file for a particular frame Rabeta Yeasmin (Tue May 16 2017 - 18:18:33 CDT)
- Howto gaussian accelerated MD Francesco Pietra (Tue May 16 2017 - 09:34:11 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: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 Vlad Cojocaru (Tue May 16 2017 - 08:20:31 CDT)
- Re: colvar distanceInv not propagated with a harmonic moving restraint in NAMD 2.12 Jérôme Hénin (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 - 09:36:38 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 - 10:50:10 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 Jérôme Hénin (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)
- [NAMD] Outputting PMF at half the time using Metadynamics The Cromicus Productions (Sun May 14 2017 - 14:04:32 CDT)
- restraining selected atom's z coordinates Rabeta Yeasmin (Sat May 13 2017 - 19:17:26 CDT)
- [NAMD] Problem with colvar "tilt" The Cromicus Productions (Fri May 12 2017 - 08:34:33 CDT)
- Pulling protein through membrane without changing the position of membrane Rabeta Yeasmin (Thu May 11 2017 - 11:51:44 CDT)
- CHARMRUN ERROR Zeki Zeybek (Thu May 11 2017 - 02:39:43 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)
- pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Mon May 08 2017 - 14:59:06 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Vermaas, Joshua (Mon May 08 2017 - 17:01:05 CDT)
- RE: pKa calculation with thermodynamic integration (TI) Radak, Brian K (Tue May 09 2017 - 10:41:52 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Wed May 10 2017 - 19:36:16 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Brian Radak (Thu May 11 2017 - 10:27:25 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Vermaas, Joshua (Thu May 11 2017 - 11:52:48 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Wed May 17 2017 - 02:00:11 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) Radak, Brian K (Wed May 17 2017 - 09:54:39 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Tue May 23 2017 - 01:04:17 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 (Wed May 24 2017 - 10:48:29 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 - 13:16:46 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 (Mon May 29 2017 - 15:45:10 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Brian Radak (Tue May 30 2017 - 09:23:34 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Sadegh Faramarzi Ganjabad (Tue May 30 2017 - 13:12:23 CDT)
- Re: pKa calculation with thermodynamic integration (TI) Vermaas, Joshua (Mon May 08 2017 - 17:01:05 CDT)
- Question about new NAMD QM/MM code Eric Smoll (Sun May 07 2017 - 22:08:08 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] How to build and simulate a periodic DNA in NAMD Nielsen, Steven (Sat May 06 2017 - 13:49:13 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 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 (Sun May 07 2017 - 00:03:43 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: [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 (Tue Jun 13 2017 - 05:42:00 CDT)
- Re: [NAMD] How to build and simulate a periodic DNA in NAMD Vermaas, Joshua (Tue Jun 13 2017 - 12:09:32 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: [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)
- 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)
- compilation of NAMD 2.12 fails Vlad Cojocaru (Thu Apr 27 2017 - 10:02:19 CDT)
- Re: compilation of NAMD 2.12 fails Vermaas, Joshua (Thu Apr 27 2017 - 11:37:08 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 Vlad Cojocaru (Fri Apr 28 2017 - 09:14:58 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 - 10:23:24 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 - 10:36:12 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 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)
- 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)
- Kinetic energy outputs matthew reeves (Thu Apr 27 2017 - 06:29:38 CDT)
- Fwd: colvars to restrain peptide close to lipid Chitrak Gupta (Wed Apr 26 2017 - 17:22:37 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)
- 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)
- 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)
- namd 2.12 and plumed 2.3 Vlad Cojocaru (Wed Apr 26 2017 - 05:20:28 CDT)
- Re: namd 2.12 and plumed 2.3 Bassam Haddad (Wed Apr 26 2017 - 10:48:55 CDT)
- Re: namd 2.12 and plumed 2.3 Vlad Cojocaru (Wed Apr 26 2017 - 11:23:54 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 Giacomo Fiorin (Wed Apr 26 2017 - 12:01:51 CDT)
- Re: namd 2.12 and plumed 2.3 Vlad Cojocaru (Tue May 02 2017 - 08:12:22 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 - 09:00:14 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 Vermaas, Joshua (Tue May 02 2017 - 10:22:01 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 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 Vlad Cojocaru (Wed Apr 26 2017 - 11:23:54 CDT)
- Re: namd 2.12 and plumed 2.3 Bassam Haddad (Wed Apr 26 2017 - 10:48:55 CDT)
- Querries on eABF Souvik Sinha (Wed Apr 26 2017 - 01:40:21 CDT)
- Re: Querries on eABF Souvik Sinha (Wed Apr 26 2017 - 06:17:03 CDT)
- Re: Querries on eABF Jérôme Hénin (Thu Apr 27 2017 - 16:00:31 CDT)
- Re: Querries on eABF Souvik Sinha (Thu May 25 2017 - 05:02:32 CDT)
- Re: Querries on eABF Jeff Comer (Thu May 25 2017 - 16:06:33 CDT)
- Re: Querries on eABF Souvik Sinha (Fri May 26 2017 - 00:45:37 CDT)
- Re: Querries on eABF Jérôme Hénin (Fri May 26 2017 - 10:30:46 CDT)
- Re: Querries on eABF Souvik Sinha (Fri May 26 2017 - 10:53:04 CDT)
- Re: Querries on eABF Souvik Sinha (Tue May 30 2017 - 02:51:31 CDT)
- Re: Querries on eABF Souvik Sinha (Tue May 30 2017 - 07:37:19 CDT)
- Re: Querries on eABF Jérôme Hénin (Tue May 30 2017 - 07:54:55 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 - 11:01:09 CDT)
- Re: Querries on eABF yjcoshc_at_gmail.com (Tue May 30 2017 - 20:18:40 CDT)
- Re: Querries on eABF Jérôme Hénin (Tue May 30 2017 - 23:10:42 CDT)
- Re: Querries on eABF Souvik Sinha (Wed Jul 12 2017 - 07:15:51 CDT)
- Re: Querries on eABF Jérôme Hénin (Wed Jul 12 2017 - 07:24:14 CDT)
- Re: Querries on eABF Souvik Sinha (Wed Jul 12 2017 - 07:34:46 CDT)
- Re: Querries on eABF Souvik Sinha (Sat Jul 15 2017 - 07:39:34 CDT)
- Re: Querries on eABF Souvik Sinha (Wed Apr 26 2017 - 06:17:03 CDT)
- NAMD developer workshop - Chicago, May 22-23, 2017 João Ribeiro (Tue Apr 25 2017 - 07:45:59 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)
- Type of solvent water molecules Oscar Bastidas (Tue Apr 18 2017 - 16:05:06 CDT)
- What to cite for CHARMM22 Oscar Bastidas (Tue Apr 18 2017 - 12:37:04 CDT)
- NAMD developer workshop - Chicago, May 22-23, 2017 João 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)
- how to have large coordinate values in the "coordinates PDB" file Nielsen, Steven (Mon Apr 17 2017 - 13:33:37 CDT)
- TCBG Live Computational Biophysics Workshop Lectures João 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)
- 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)
- Neutralize a box for FEP David Huggins (Wed Apr 12 2017 - 10:30:20 CDT)
- Incorporate aluminum oxide monolayer The Cromicus Productions (Tue Apr 11 2017 - 14:50:37 CDT)
- lipid centering Mihaela Drenscko (Tue Apr 11 2017 - 13:08:24 CDT)
- TCBG Live Computational Biophysics Workshop Lectures João Ribeiro (Mon Apr 10 2017 - 08:24:13 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)
- 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)
- 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)
- patch hem_chandra_at_iitg.ernet.in (Fri Mar 31 2017 - 04:03:15 CDT)
- Fatal Error in NAMD Faramarz Joodaki (Thu Mar 30 2017 - 12:14:51 CDT)
- patch hem_chandra_at_iitg.ernet.in (Mon Mar 27 2017 - 23:28:53 CDT)
- Solvent box fluctuations Götz, 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)
- (no subject) Marco Antonio Ramirez Martinez (Thu Mar 23 2017 - 13:23:33 CDT)
- Scaling behaviour of NAMD on hosts with GPU accelrators Kraus, Sebastian (Thu Mar 23 2017 - 11:18:14 CDT)
- Re: Scaling behaviour of NAMD on hosts with GPU accelrators Jeff Comer (Thu Mar 23 2017 - 12:24:23 CDT)
- AW: Scaling behaviour of NAMD on hosts with GPU accelrators Norman Geist (Fri Mar 24 2017 - 05:27:46 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 - 05:47:39 CDT)
- Re: AW: Scaling behaviour of NAMD on hosts with GPU accelrators Maxime Boissonneault (Fri Mar 24 2017 - 06:42:04 CDT)
- Re: Scaling behaviour of NAMD on hosts with GPU accelrators Boonstra, S. (Fri Mar 24 2017 - 06:41:19 CDT)
- AW: Scaling behaviour of NAMD on hosts with GPU accelrators Norman Geist (Fri Mar 24 2017 - 05:35:00 CDT)
- Explanation of parameters for NBTABLE's tabulated external file? Wasut Pornpatcharapong (Wed Mar 22 2017 - 12:55:12 CDT)
- Re: Explanation of parameters for NBTABLE's tabulated external file? Vermaas, Joshua (Wed Mar 22 2017 - 13:09:02 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? David Hardy (Wed Mar 22 2017 - 14:09:17 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? Wasut Pornpatcharapong (Wed Mar 22 2017 - 16:59:19 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)
- Hands-On Workshop on Computational Biophysics: May 30 - June 2 in Pittsburgh, PA João Ribeiro KS (Wed Mar 22 2017 - 10:15:40 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: 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)
- Defining colvars based on a region Bob Faith (Mon Mar 20 2017 - 19:48:00 CDT)
- Problem with namd2 execution on Windows GPU version md_at_novamechanics.com (Fri Mar 17 2017 - 15:57:26 CDT)
- problem to generate LPS PSF file using PSFGEN 송연호 (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)
- Some questions about the orthogonality of colvars in ABF. yjcoshc (Wed Mar 15 2017 - 07:11:46 CDT)
- 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)
- Specify number of water molecules:simulation set up in VMD Rabeta Yeasmin (Fri Mar 10 2017 - 13:21:31 CST)
- NAMD-2.12 handful of issues with CUDA Norman Geist (Fri Mar 10 2017 - 03:16:13 CST)
- specify H-bond in CGMD Deng, Jinxia (Nancy) (Thu Mar 09 2017 - 08:42:14 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)
- 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: problems mutating HID to TYR for free energy calculations Radak, Brian K (Tue Mar 07 2017 - 09:49:38 CST)
- Re: problems mutating HID to TYR for free energy calculations Nehad Elsalamouny (Tue Mar 07 2017 - 16:50:32 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 - 17:39:37 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 - 16:50:32 CST)
- RE: problems mutating HID to TYR for free energy calculations Radak, Brian K (Tue Mar 07 2017 - 09:49:38 CST)
- Question about applying external force The Cromicus Productions (Mon Mar 06 2017 - 13:56:30 CST)
- Re: Question about applying external force Jérôme Hénin (Mon Mar 06 2017 - 14:23:24 CST)
- Re: Question about applying external force The Cromicus Productions (Mon Mar 06 2017 - 15:32:36 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 - 15:59:25 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 - 18:27:20 CST)
- Re: Question about applying external force The Cromicus Productions (Mon Mar 06 2017 - 15:32:36 CST)
- Re: Question about applying external force Jérôme Hénin (Mon Mar 06 2017 - 14:23:24 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)
- REMD on HPC HOUSTON Douglas (Mon Mar 06 2017 - 08:15:25 CST)
- Workshop on Computational Biophysics, Urbana, IL: Application Deadline March 10th João 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)
- 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 João Ribeiro KS (Fri Feb 24 2017 - 19:23:08 CST)
- colvars not scaling well in NAMD 2.10 Chitrak Gupta (Thu Feb 23 2017 - 17:25:14 CST)
- torsional restrain Lara rajam (Thu Feb 23 2017 - 10:14:21 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: colvars: Error: Feature unavailable:compute total collective force only from one group center Ajasja Ljubetič (Thu Feb 23 2017 - 01:36:03 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: colvars: Error: Feature unavailable:compute total collective force only from one group center Bennion, Brian (Thu Feb 23 2017 - 10:38:39 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: colvars: Error: Feature unavailable:compute total collective force only from one group center Giacomo Fiorin (Thu Feb 23 2017 - 14:44:00 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 Giacomo Fiorin (Thu Feb 23 2017 - 21:50:08 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: colvars: Error: Feature unavailable:compute total collective force only from one group center Bennion, Brian (Mon Feb 27 2017 - 17:36:53 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 Giacomo Fiorin (Thu Feb 23 2017 - 03:10:20 CST)
- Re: colvars: Error: Feature unavailable:compute total collective force only from one group center Ajasja Ljubetič (Thu Feb 23 2017 - 01:36:03 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)
- 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)
- Charm++ Fatal Error Question Oscar Bastidas (Mon Feb 20 2017 - 11:36:53 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 João 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)
- 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)
- question about Steered Molecular Dynamics Oleksii Zdorevskyi (Wed Feb 15 2017 - 08:38:22 CST)
- Fixing COM of one atom in selection and letting the other move Life Sciences Inc (Tue Feb 14 2017 - 12:15:00 CST)
- [NAMD] Obtain dynamical matrix away from equilibrium The Cromicus Productions (Thu Feb 09 2017 - 12:02:35 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)
- 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)
- 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)
- 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)
- 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)
- ++idlepoll Zeki Zeybek (Mon Feb 06 2017 - 01:21:19 CST)
- strange diffs in energy output of NAMD 2.9 vs. 2.11 Erik Nordgren (Fri Feb 03 2017 - 14:05:23 CST)
- High pressure calculations faride badalkhani (Fri Feb 03 2017 - 10:10:39 CST)
- Re: High pressure calculations Vermaas, Joshua (Fri Feb 03 2017 - 11:15:04 CST)
- Re: High pressure calculations faride badalkhani (Fri Feb 03 2017 - 13:23:34 CST)
- AW: High pressure calculations Norman Geist (Sat Feb 04 2017 - 05:33:49 CST)
- Re: AW: High pressure calculations Andrey KALINICHEV (Sat Feb 04 2017 - 05:54:36 CST)
- Re: AW: High pressure calculations Francesco Pietra (Sat Feb 04 2017 - 06:00:53 CST)
- Re: AW: High pressure calculations faride badalkhani (Sat Feb 04 2017 - 06:11:52 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)
- Positions for Ph.D. candidates in biomolecular modeling Jan Brezovsky (Thu Feb 02 2017 - 05:30:48 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)
- Inconsistency between NAMD 2.11 and NAMD 2.12 Bryan Roessler (Tue Jan 31 2017 - 00:52:22 CST)
- AW: AW: AW: not a number in NAMD log file Norman Geist (Mon Jan 30 2017 - 01:44:14 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)
- On-the-fly eABF: Problem with the tcl script. Emmanuel MOUTOUSSAMY (Thu Jan 26 2017 - 06:06:52 CST)
- basis set for QM-MM dft Francesco Pietra (Wed Jan 25 2017 - 09:15:43 CST)
- how do I restart umbrella sampling calculations? Olya Kravchenko (Tue Jan 24 2017 - 14:39:12 CST)
- Re: how do I restart umbrella sampling calculations? Giacomo Fiorin (Tue Jan 24 2017 - 14:50:41 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? Giacomo Fiorin (Tue Jan 24 2017 - 15:20:38 CST)
- Re: how do I restart umbrella sampling calculations? Olya Kravchenko (Tue Jan 24 2017 - 15:44:32 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 - 16:11:17 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 (Wed Jan 25 2017 - 09:19:10 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)
- [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)
- minimizing each structure of a DCD file saeed amini (Sun Jan 22 2017 - 07:21:23 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)
- Energy Gradient Plotting Zeki Zeybek (Wed Jan 18 2017 - 02:19:03 CST)
- Drude minimization does not converge Christian Jorgensen (Fri Jan 13 2017 - 10:16:08 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)
- NAMD performance monitor Nikhil Maroli (Tue Jan 17 2017 - 06:42:41 CST)
- QM-MM ORCA Charm++ error Could not find QM output file Francesco Pietra (Mon Jan 16 2017 - 01:55:38 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: QM-MM ORCA Charm++ error Could not find QM output file Francesco Pietra (Tue Jan 17 2017 - 12:10:52 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: QM-MM ORCA Charm++ error Could not find QM output file Francesco Pietra (Thu Jan 19 2017 - 11:56:20 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 (Tue Jan 17 2017 - 12:10:52 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)
- Drude minimization does not converge Christian Jorgensen (Fri Jan 13 2017 - 10:19:03 CST)
- How to get ideal alpha-helical, ω-shaped γ-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)
- 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)
- fatal error in running namd/2.12 sunyeping (Wed Jan 11 2017 - 07:46:01 CST)
- Solvation free energy difference of alchemical transformation of K+ into Na+ Abhishek Kumar Singh (Tue Jan 10 2017 - 05:09:01 CST)
- Re: Solvation free energy difference of alchemical transformation of K+ into Na+ Hannes Loeffler (Tue Jan 10 2017 - 06:15:02 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: 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+ Radak, Brian K (Tue Jan 10 2017 - 12:27:07 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+ Abhishek Kumar Singh (Wed Jan 11 2017 - 00:39:11 CST)
- Re: Solvation free energy difference of alchemical transformation of K+ into Na+ Brian Radak (Wed Jan 11 2017 - 10:20:21 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: Solvation free energy difference of alchemical transformation of K+ into Na+ Hannes Loeffler (Tue Jan 10 2017 - 06:15:02 CST)
- Charm++ fatal error with QM-MM MOPAC Francesco Pietra (Tue Jan 10 2017 - 01:56:35 CST)
- Re: Charm++ fatal error with QM-MM MOPAC Marcelo C. R. Melo (Tue Jan 10 2017 - 08:11:02 CST)
- The reason for the formation of bubbles in heating stage Mohaddeseh Habibzadeh (Mon Jan 09 2017 - 08:16:51 CST)
- not a number error Mohaddeseh Habibzadeh (Mon Jan 09 2017 - 01:53:08 CST)
- Solvation free energy difference of alchemical transformation of K+ into Na+ Abhishek Kumar Singh (Mon Jan 09 2017 - 00:09:32 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)
- readable output of gbis.coor hem_chandra_at_iitg.ernet.in (Sat Jan 07 2017 - 00:43:19 CST)
- very small cell 小澤友 (Fri Jan 06 2017 - 20:29:34 CST)
- multiple replicas metadynamics Mihaela Drenscko (Fri Jan 06 2017 - 20:24:46 CST)
- Re: multiple replicas metadynamics Giacomo Fiorin (Sun Jan 08 2017 - 17:37:21 CST)
- Re: multiple replicas metadynamics Mihaela Drenscko (Mon Jan 09 2017 - 16:02:45 CST)
- Regarding: Free energy of alchemical transformation of K + and Na + Amit Kumar (Fri Jan 06 2017 - 05:09:35 CST)
- Constraining bonds that don't include hydrogens Marlon Sidore (Thu Jan 05 2017 - 08:11:06 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)
- 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)
- MD using implicit solvent hem_chandra_at_iitg.ernet.in (Fri Dec 30 2016 - 05:51:58 CST)
- Problems running NAMD QM-MM with ORCA 3.0.3 Francesco Pietra (Fri Dec 30 2016 - 03:24:04 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)
- NAMD 2.12 released Angelo Rossi (Mon Dec 26 2016 - 15:53:42 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)
- Modifying equilibrium distance for a specific region of carbon nanotube in the parameter file jashnvareh 1395 (Mon Dec 26 2016 - 08:30:59 CST)
- Query regarding colvar distanceZ Peter Mawanga (Mon Dec 26 2016 - 06:57:57 CST)
- Re: Query regarding colvar distanceZ Vermaas, Joshua (Mon Dec 26 2016 - 08:12:23 CST)
- Re: Query regarding colvar distanceZ Peter Mawanga (Mon Dec 26 2016 - 09:07:18 CST)
- Re: Query regarding colvar distanceZ Peter Mawanga (Mon Dec 26 2016 - 09:17:34 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 - 11:39:48 CST)
- Re: Query regarding colvar distanceZ Giacomo Fiorin (Tue Dec 27 2016 - 13:20:42 CST)
- Re: Query regarding colvar distanceZ Peter Mawanga (Tue Dec 27 2016 - 19:07:07 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 - 20:47:16 CST)
- Re: Query regarding colvar distanceZ Peter Mawanga (Mon Dec 26 2016 - 09:07:18 CST)
- Re: Query regarding colvar distanceZ Vermaas, Joshua (Mon Dec 26 2016 - 08:12:23 CST)
- Regarding Trajectory files Amit Kumar (Sun Dec 25 2016 - 23:18:26 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)
- 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)
- NAMD 2.12 released Jim Phillips (Fri Dec 23 2016 - 12:57:34 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)
- 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)
- Studying Folding of 870 Small Peptides. Computationally Feasible? Eric A Brenner (Sat Dec 17 2016 - 12:35:59 CST)
- Re: Studying Folding of 870 Small Peptides. Computationally Feasible? JC Gumbart (Sat Dec 17 2016 - 18:48:50 CST)
- Writing number of atoms in a specific group to a file Hamed Fadaei (Fri Dec 16 2016 - 11:35:24 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)
- psfgen - pdbalias when using readpsf Brian Radak (Thu Dec 15 2016 - 14:28:56 CST)
- NAMD Energies Chris Goedde (Wed Dec 14 2016 - 13:13:01 CST)
- using colvars to constrain two atoms in a direction Hamed Fadaei (Wed Dec 14 2016 - 10:15:20 CST)
- Re: using colvars to constrain two atoms in a direction Giacomo Fiorin (Wed Dec 14 2016 - 10:22:39 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 - 10:40:57 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 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 - 11:11:00 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)
- A problem in ABF simulation 宋瑞珩 (Wed Dec 14 2016 - 05:45:28 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)
- protonating ASP and GLU Nehad Elsalamouny (Tue Dec 13 2016 - 05:58:51 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)
- FATAL ERROR: Duplicate bond when going from nvt to npt Marlon Sidore (Mon Dec 12 2016 - 04:02:17 CST)
- (no subject) Tom King (Fri Dec 09 2016 - 16:43:07 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)
- Problem with alpha colvar in NAMD 2.12b1 Amy Rice (Thu Dec 08 2016 - 15:23:16 CST)
- (no subject) Nehir NALINCI (Thu Dec 08 2016 - 01:06:44 CST)
- NAMD How to calculate ns/day Jan Fredin (Wed Dec 07 2016 - 16:02:16 CST)
- Returning energy values from .log file. matthew reeves (Wed Dec 07 2016 - 14:16:44 CST)
- Minimization error Santanu Santra (Tue Dec 06 2016 - 23:00:04 CST)
- Energy output values matthew reeves (Tue Dec 06 2016 - 13:16:00 CST)
- selectively assign HIE or HID for HIS residues Nehad Elsalamouny (Mon Dec 05 2016 - 20:19:44 CST)
- Getting cluster with defined criteria Peter Mawanga (Sun Dec 04 2016 - 07:05:35 CST)
- How to continue RMSD of previous production simulation Farhad Jahanfar (Fri Dec 02 2016 - 12:21:36 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)
- Amber forcefield in namd simulation in parallel version Santanu Santra (Thu Dec 01 2016 - 06:36:24 CST)
- AW: Amber forcefield in namd simulation in parallel version Norman Geist (Thu Dec 01 2016 - 07:58:00 CST)
- Re: Amber forcefield in namd simulation in parallel version Santanu Santra (Thu Dec 01 2016 - 23:00:45 CST)
- Re: Amber forcefield in namd simulation in parallel version Santanu Santra (Fri Dec 02 2016 - 00:05:35 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 Teerapong Pirojsirikul (Fri Dec 02 2016 - 03:30:11 CST)
- Re: Amber forcefield in namd simulation in parallel version Santanu Santra (Thu Dec 01 2016 - 23:00:45 CST)
- AW: Amber forcefield in namd simulation in parallel version Norman Geist (Thu Dec 01 2016 - 07:58:00 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)
- query on OuputTotalforce Vs OnesiteTotal force ? Bala subramanian (Tue Nov 29 2016 - 09:39:39 CST)
- A problem in ABF simulation 宋瑞珩 (Tue Nov 29 2016 - 04:28:21 CST)
- How to create 3'-3' phosphodiester linkage for a DNA. Susmita Ghosh (Mon Nov 28 2016 - 23:50:26 CST)
- NVE simulations in NAMD - the right choice of timesteps and parameters Harish Srinivasan (Tue Nov 29 2016 - 04:54:32 CST)
- Running gromacs in namd Subbarao Kanchi (Tue Nov 29 2016 - 00:30:37 CST)
- AW: Running gromacs in namd Norman Geist (Tue Nov 29 2016 - 01:36:48 CST)
- Re: Running gromacs in namd Subbarao Kanchi (Tue Nov 29 2016 - 04:25:06 CST)
- AW: Running gromacs in namd Norman Geist (Wed Nov 30 2016 - 02:45:09 CST)
- Re: Running gromacs in namd Subbarao Kanchi (Thu Dec 01 2016 - 00:27:37 CST)
- AW: Running gromacs in namd Norman Geist (Thu Dec 01 2016 - 01:06:23 CST)
- Re: Running gromacs in namd Subbarao Kanchi (Thu Dec 01 2016 - 01:42:24 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)
- tclBC during SMD and ABF simulations Olya Kravchenko (Mon Nov 28 2016 - 12:36:47 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)
- Ligand jump out of the protein through NPT ensemle runs mahdi K (Fri Nov 25 2016 - 06:40:31 CST)
- Low global exclusion count errors! faride badalkhani (Thu Nov 24 2016 - 10:28:53 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: Simulation of metalo-binding proteins Jérôme Hénin (Wed Nov 23 2016 - 14:11:44 CST)
- AW: Simulation of metalo-binding proteins Daniel Möller (Wed Nov 23 2016 - 15:52:53 CST)
- Re: Simulation of metalo-binding proteins James Starlight (Thu Nov 24 2016 - 14:01:08 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 - 14:44:03 CST)
- Re: Simulation of metalo-binding proteins luca belmonte (Fri Nov 25 2016 - 06:47:10 CST)
- AW: Simulation of metalo-binding proteins Daniel Möller (Wed Nov 23 2016 - 15:52:53 CST)
- Re: Simulation of metalo-binding proteins Jérôme Hénin (Wed Nov 23 2016 - 14:11:44 CST)
- Separate switchdist for electrostatic interactions Peter Mawanga (Mon Nov 21 2016 - 06:17:18 CST)
- “Cannot 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)
- Query on colvar distanceZ Bala subramanian (Sat Nov 19 2016 - 08:18:57 CST)
- Pressure Profile. msa5 (Thu Nov 17 2016 - 11:06:48 CST)
- Generate psf file in x-plor format Nehad Elsalamouny (Thu Nov 17 2016 - 06:07:39 CST)
- Re: Generate psf file in x-plor format Vermaas, Joshua (Thu Nov 17 2016 - 09:47:42 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)
- 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 Vermaas, Joshua (Thu Nov 17 2016 - 18:56:55 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 Nehad Elsalamouny (Thu Nov 17 2016 - 14:44:40 CST)
- Re: Generate psf file in x-plor format Vermaas, Joshua (Thu Nov 17 2016 - 09:47:42 CST)
- NAMD GPU+ibverbs on multiple nodes: timeout problems Robert Sawko (Thu Nov 17 2016 - 05:51:21 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)
- Crashes with dihedral PC Jiyong Park (Tue Nov 15 2016 - 20:28:32 CST)
- Re: Queries regarding metadynamics and .pmf visualization Giacomo Fiorin (Tue Nov 15 2016 - 10:40:15 CST)
- SMD restraints Allen, Caley R (Mon Nov 14 2016 - 15:14:09 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)
- NAMD2.12b1 and CUDA Jeff Comer (Thu Nov 10 2016 - 09:09:50 CST)
- restraint backbone to keep secondary structure in coarse grain MD Deng, Jinxia (Nancy) (Wed Nov 09 2016 - 10:42:46 CST)
- About pbc Francesco Pietra (Tue Nov 08 2016 - 15:10:56 CST)
- Trigger DCD frame from TCL? Norman Geist (Tue Nov 08 2016 - 09:12:04 CST)
- Re: Trigger DCD frame from TCL? Brian Radak (Tue Nov 08 2016 - 09:22:24 CST)
- AW: Trigger DCD frame from TCL? Norman Geist (Wed Nov 09 2016 - 02:05:50 CST)
- AW: Trigger DCD frame from TCL? Norman Geist (Wed Nov 09 2016 - 02:48:33 CST)
- Re: AW: Trigger DCD frame from TCL? Brian Radak (Wed Nov 09 2016 - 07:34:48 CST)
- Re: AW: Trigger DCD frame from TCL? Jim Phillips (Wed Nov 09 2016 - 16:48:00 CST)
- AW: AW: Trigger DCD frame from TCL? Norman Geist (Thu Nov 10 2016 - 02:09:22 CST)
- AW: Trigger DCD frame from TCL? Norman Geist (Wed Nov 09 2016 - 02:05:50 CST)
- Re: Trigger DCD frame from TCL? Brian Radak (Tue Nov 08 2016 - 09:22:24 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)
- 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)
- 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)
- 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)
- no response from mail list sunyeping (Mon Oct 31 2016 - 19:23:09 CDT)
- is it possible to restrict the access of ions to certain volume? Olya Kravchenko (Mon Oct 31 2016 - 15:28:40 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)
- 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)
- 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)
- Switch off rescale temperature after some number of timesteps Harish Srinivasan (Wed Oct 26 2016 - 01:05:50 CDT)
- fix disulfide bond in coarse grain(CG) model for NAMD Deng, Jinxia (Nancy) (Mon Oct 24 2016 - 11:46:11 CDT)
- Using NAMD with NMR structure Oscar Bastidas (Sun Oct 23 2016 - 02:00:14 CDT)
- NAMD breaks with wrong timestep Gtz, Alexander (Fri Oct 21 2016 - 08:23:33 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)
- Minimization failing on one machine only Chris Goedde (Fri Oct 14 2016 - 15:34:10 CDT)
- Collecting average energies via Tcl callback? Brian Radak (Thu Oct 13 2016 - 11:19:40 CDT)
- visualizing and analyzing long simulation Dhiraj Srivastava (Mon Oct 10 2016 - 10:41:53 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 孙业平 (Sun Oct 09 2016 - 14:09:47 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)
- Re: question regarding rmsd Pardis Tabaee (Wed Oct 05 2016 - 10:55:01 CDT)
- Re: question regarding rmsd dhirajks_at_gmail.com (Wed Oct 05 2016 - 11:03:41 CDT)
- Re: question regarding rmsd Roshan Shrestha (Wed Oct 05 2016 - 11:07:09 CDT)
- RE: question regarding rmsd Radak, Brian K (Wed Oct 05 2016 - 11:18:12 CDT)
- Re: question regarding rmsd Pardis Tabaee (Wed Oct 05 2016 - 13:34:41 CDT)
- Re: question regarding rmsd Dhiraj Srivastava (Wed Oct 05 2016 - 14:02:32 CDT)
- RE: question regarding rmsd Radak, Brian K (Wed Oct 05 2016 - 15:39:01 CDT)
- Re: question regarding rmsd Leandro Martínez (Wed Oct 05 2016 - 15:58:39 CDT)
- Re: question regarding rmsd dhirajks_at_gmail.com (Thu Oct 06 2016 - 17:37:23 CDT)
- Re: question regarding rmsd dhirajks_at_gmail.com (Wed Oct 05 2016 - 11:03:41 CDT)
- Re: question regarding rmsd Pardis Tabaee (Wed Oct 05 2016 - 10:55:01 CDT)
- Tcl clock Laura Joana (Tue Oct 04 2016 - 14:10:12 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)
- Oxidized cysteine parameters for CHARMM36 Gergely Gyimesi (Fri Sep 30 2016 - 08:40:04 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)
- Wrapall on or off? sunyeping (Tue Sep 27 2016 - 00:14:49 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)
- 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)
- 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)
- 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)
- 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)
- Umbrella sampling colvars DistanceZ deviates a lot Kevin C Chan (Tue Sep 13 2016 - 11:19:08 CDT)
- Re: Umbrella sampling colvars DistanceZ deviates a lot Giacomo Fiorin (Tue Sep 13 2016 - 11:23:56 CDT)
- Re: Umbrella sampling colvars DistanceZ deviates a lot Tabris Chun Chan (Tue Sep 13 2016 - 12:27:25 CDT)
- Re: Umbrella sampling colvars DistanceZ deviates a lot Giacomo Fiorin (Tue Sep 13 2016 - 15:16:14 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 Kevin C Chan (Tue Sep 13 2016 - 23:10:21 CDT)
- Re: Umbrella sampling colvars DistanceZ deviates a lot Giacomo Fiorin (Wed Sep 14 2016 - 08:32:43 CDT)
- Re: Umbrella sampling colvars DistanceZ deviates a lot Tabris Chun Chan (Tue Sep 13 2016 - 12:27:25 CDT)
- Re: Umbrella sampling colvars DistanceZ deviates a lot Giacomo Fiorin (Tue Sep 13 2016 - 11:23:56 CDT)
- Gradual Heating Periodic Error Jackson Cavett (Tue Sep 13 2016 - 08:34:30 CDT)
- PMF decompostion Azadeh Alavi (Mon Sep 12 2016 - 06:49:50 CDT)
- AW: REMD and sortreplicas program Norman Geist (Mon Sep 12 2016 - 01:05:39 CDT)
- Shear Stress modelling in NAMD James Starlight (Sun Sep 11 2016 - 05:12:26 CDT)
- Simulated annealing, in solvent or in vacuum? faride badalkhani (Thu Sep 08 2016 - 14:21:26 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)
- Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 04:54:35 CDT)
- Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 00:12:37 CDT)
- Re: Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 02:36:31 CDT)
- Re: Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 11:01:22 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 Vermaas, Joshua (Thu Sep 08 2016 - 11:19:05 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 Mahrukh Imtiaz (Thu Sep 08 2016 - 11:01:22 CDT)
- Re: Query regarding parameter file generation of non standard residue Mahrukh Imtiaz (Thu Sep 08 2016 - 02:36:31 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)
- Query regarding parameter file generation of a non standard residue Mahrukh Imtiaz (Wed Sep 07 2016 - 15:12:14 CDT)
- The needed time for a MD simulation faride badalkhani (Mon Sep 05 2016 - 10:11:08 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)
- did anyone built NAMD with PLUMED on XSEDE Maksym Korablyov (Thu Sep 01 2016 - 09:36:07 CDT)
- FATAL ERROR CUDA error during equilibration using NAMD Abraham A. Gutierrez Hernandez (Tue Aug 30 2016 - 18:27:38 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)
- targetCenters in Umbrella Sampling Olya Kravchenko (Wed Aug 24 2016 - 17:50:36 CDT)
- interpretation of eigenvec colvar? JC Gumbart (Tue Aug 23 2016 - 20:02:37 CDT)
- Shrinking a molecule (Colvars and Constant Pressure not working) Sonu Kumar (Mon Aug 22 2016 - 15:21:48 CDT)
- PMF calculation input files Olya Kravchenko (Mon Aug 22 2016 - 10:30:28 CDT)
- Re: PMF calculation input files Vermaas, Joshua (Mon Aug 22 2016 - 11:23:58 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 - 16:27:34 CDT)
- Re: PMF calculation input files Olya Kravchenko (Tue Aug 23 2016 - 10:01:05 CDT)
- Re: PMF calculation input files Vermaas, Joshua (Tue Aug 23 2016 - 11:02:01 CDT)
- Re: PMF calculation input files Olya Kravchenko (Wed Aug 24 2016 - 16:23:30 CDT)
- Re: PMF calculation input files Jérôme Hénin (Wed Aug 24 2016 - 15:22:47 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)
- NAMD equilibrium step d.ronika_at_iitg.ernet.in (Mon Aug 22 2016 - 00:34:01 CDT)
- Graphene Oxide Parameter File Marisol Oswald (Sat Aug 20 2016 - 14:25:38 CDT)
- how to rerun a namd trajectory in order to complement the missing snapshots? sunyeping (Thu Aug 18 2016 - 22:35:51 CDT)
- Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Thu Aug 18 2016 - 04:21:07 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Thu Aug 18 2016 - 09:47:02 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 - 10:21:30 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 - 11:00:16 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 - 11:20:22 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 faride badalkhani (Thu Aug 18 2016 - 11:31:05 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 (Mon Aug 22 2016 - 07:34:17 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Tue Aug 23 2016 - 13:59:31 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 - 14:28:36 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero faride badalkhani (Mon Sep 05 2016 - 06:03:13 CDT)
- Re: Autocorrelation function of Rg goes down without fluctuation around zero Brian Radak (Tue Sep 06 2016 - 16:43:30 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 (Wed Sep 07 2016 - 09:17:03 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 faride badalkhani (Thu Aug 18 2016 - 13:50:23 CDT)
- RE: Autocorrelation function of Rg goes down without fluctuation around zero Lennart Nilsson (Fri Aug 19 2016 - 01:42:03 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 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)
- 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)
- 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)
- Energy minimization d.ronika_at_iitg.ernet.in (Mon Aug 15 2016 - 00:05:12 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)
- Is it possible to perform NVT FEP on a fluid system? B.W.J. Irwin (Tue Aug 09 2016 - 05:22:08 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)
- How to replace NAMD Eletrostatic Forces Emerson Macedo (Thu Aug 04 2016 - 13:15:38 CDT)
- Re: How to replace NAMD Eletrostatic Forces Brian Radak (Thu Aug 04 2016 - 15:17:17 CDT)
- Re: How to replace NAMD Eletrostatic Forces Jérôme Hénin (Thu Aug 04 2016 - 17:21:40 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 Ajasja Ljubetič (Fri Aug 05 2016 - 02:46:00 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 Emerson Macedo (Fri Aug 05 2016 - 10:45:12 CDT)
- Re: How to replace NAMD Eletrostatic Forces Jérôme Hénin (Thu Aug 04 2016 - 17:21:40 CDT)
- Re: How to replace NAMD Eletrostatic Forces Brian Radak (Thu Aug 04 2016 - 15:17:17 CDT)
- Fatal Error: vdw atom type CC3161 Allen, Caley R (Wed Aug 03 2016 - 09:53:37 CDT)
- Maximum dihedral angle Mahdi Tavakol (Sun Jul 31 2016 - 03:19:16 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)
- Re: Generalized Born solvation models supported by NAMD Aron Broom (Fri Jul 29 2016 - 10:55:51 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 - 12:25:49 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 - 14:24:21 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 (Tue Aug 02 2016 - 09:41:09 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 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)
- water permeation through nanotube in lipid bilayer Nikhil Maroli (Fri Jul 29 2016 - 07:18:45 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)
- (no subject) krishna (Tue Jul 26 2016 - 00:56:38 CDT)
- Msd Mahdiye Azadpour (Sat Jul 23 2016 - 23:21:09 CDT)
- Equivalent of gromacs' "rdd" option Marlon Sidore (Fri Jul 22 2016 - 10:12:47 CDT)
- Re: Equivalent of gromacs' "rdd" option Marlon Sidore (Fri Jul 22 2016 - 10:16:57 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 (Mon Jul 25 2016 - 02:56:06 CDT)
- Re: Equivalent of gromacs' "rdd" option Fotis Baltoumas (Mon Jul 25 2016 - 10:08:18 CDT)
- Re: Equivalent of gromacs' "rdd" option Fotis Baltoumas (Mon Jul 25 2016 - 10:26:05 CDT)
- Re: Equivalent of gromacs' "rdd" option Marlon Sidore (Mon Jul 25 2016 - 10:44:48 CDT)
- Re: Equivalent of gromacs' "rdd" option Axel Kohlmeyer (Mon Jul 25 2016 - 10:16:08 CDT)
- Re: Equivalent of gromacs' "rdd" option Marlon Sidore (Mon Jul 25 2016 - 02:56:06 CDT)
- Repulsion of lipid bilayer during equilibration Mahrukh Imtiaz (Fri Jul 22 2016 - 05:00:41 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)
- 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)
- (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)
- namd2 seg fault NAMD_2.11_Source Linux-x86_64-g++ Doug Stetner (Tue Jul 12 2016 - 22:51:40 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)
- 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)
- get seed Laura Joana (Fri Jul 01 2016 - 11:52:46 CDT)
- unbinding free energy using ABF Gabriel Jara (Thu Jun 30 2016 - 13:25:27 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)
- 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: PMF with ABF for ion channels in a spherical molecule Aron Broom (Sun Jun 26 2016 - 15:13:36 CDT)
- Re: PMF with ABF for ion channels in a spherical molecule Olya Kravchenko (Tue Jun 28 2016 - 15:35:53 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 - 16:20:13 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 (Fri Jul 01 2016 - 15:50:15 CDT)
- Re: PMF with ABF for ion channels in a spherical molecule Aron Broom (Fri Jul 01 2016 - 18:42:21 CDT)
- Re: PMF with ABF for ion channels in a spherical molecule Olya Kravchenko (Tue Jun 28 2016 - 15:35:53 CDT)
- Re: PMF with ABF for ion channels in a spherical molecule Aron Broom (Sun Jun 26 2016 - 15:13:36 CDT)
- transition metal parameters Francesca Lnstad Bleken (Fri Jun 24 2016 - 02:19:01 CDT)
- Exit Command Failure Sarah Sweger (Thu Jun 23 2016 - 08:01:09 CDT)
- The question about Network calculation ľ (Thu Jun 23 2016 - 03:28:47 CDT)
- LJcorrection option in NAMD Yue Qian (Mon Jun 20 2016 - 17:09:04 CDT)
- Re: LJcorrection option in NAMD Brian Radak (Tue Jun 21 2016 - 07:36:06 CDT)
- Re: LJcorrection option in NAMD Jérôme Hénin (Tue Jun 21 2016 - 09:48:12 CDT)
- Re: LJcorrection option in NAMD Grace Brannigan (Tue Jun 21 2016 - 13:03:24 CDT)
- Re: LJcorrection option in NAMD Brian Radak (Wed Jun 22 2016 - 17:22:07 CDT)
- Re: LJcorrection option in NAMD JC Gumbart (Mon Jun 27 2016 - 00:23:12 CDT)
- Re: LJcorrection option in NAMD Grace Brannigan (Mon Jun 27 2016 - 06:41:33 CDT)
- Re: LJcorrection option in NAMD Brian Radak (Wed Jun 22 2016 - 17:04:02 CDT)
- Re: LJcorrection option in NAMD Jérôme Hénin (Tue Jun 21 2016 - 09:48:12 CDT)
- Re: LJcorrection option in NAMD Brian Radak (Tue Jun 21 2016 - 07:36:06 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)
- namd2 or charmrun ++local ? Laura Joana (Fri Jun 17 2016 - 11:35:05 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)
- Free energy calculation using MM-GBSA with NAMD Sneha Menon (Wed Jun 15 2016 - 05:50:41 CDT)
- Missing atom type for hydroperoxide Jean-François 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)
- 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 henyi (Thu Jun 09 2016 - 15:17:25 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)
- cgenff Benjamin Hill (Mon Jun 06 2016 - 14:48:30 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)
- Unable to compile Tachyon on Sun Grid Engine Sourav Ray (Sat Jun 04 2016 - 04:20:29 CDT)
- Is GPU double-precision floating point performance important for NAMD? Mert Gür (Thu Jun 02 2016 - 16:48:07 CDT)
- autocorrelation function faride badalkhani (Thu Jun 02 2016 - 09:06:04 CDT)
- download stmv files for benchmarking Bennion, Brian (Wed Jun 01 2016 - 14:29:22 CDT)
- non-standard solvants faride badalkhani (Wed Jun 01 2016 - 11:55:28 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)
- (no subject) Srijita Paul (Tue May 31 2016 - 05:03:47 CDT)
- Replica Exchange: Equilibrating at each temperature Horia Jalily Hasani (Mon May 30 2016 - 11:28:24 CDT)
- AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Tue May 31 2016 - 04:24:52 CDT)
- AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Tue May 31 2016 - 08:41:23 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 (Thu Jun 02 2016 - 01:33:55 CDT)
- Re: AW: Replica Exchange: Equilibrating at each temperature Horia Jalily Hasani (Thu Jun 02 2016 - 10:59:56 CDT)
- AW: AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Fri Jun 03 2016 - 01:39:54 CDT)
- Re: AW: Replica Exchange: Equilibrating at each temperature Horia Jalily Hasani (Tue Jun 07 2016 - 11:21:09 CDT)
- AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Tue May 31 2016 - 08:41:23 CDT)
- AW: Replica Exchange: Equilibrating at each temperature Norman Geist (Tue May 31 2016 - 04:24:52 CDT)
- SMD simulation problem. Shambo Hore (Sun May 29 2016 - 20:15:57 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)
- Applying "selectionRule" in Multiple Walker ABF Souvik Sinha (Fri May 27 2016 - 09:43:28 CDT)
- No parameter for ribose ring, Charmm 27 Lennart Nilsson (Fri May 27 2016 - 05:42:02 CDT)
- No parameter for ribose ring, Charmm 27 Benjamin Hill (Thu May 26 2016 - 17:18:43 CDT)
- Re: No parameter for ribose ring, Charmm 27 JC Gumbart (Thu May 26 2016 - 18:42:52 CDT)
- Re: No parameter for ribose ring, Charmm 27 Benjamin Hill (Fri May 27 2016 - 05:51:40 CDT)
- Re: No parameter for ribose ring, Charmm 27 JC Gumbart (Fri May 27 2016 - 14:14:17 CDT)
- RE: No parameter for ribose ring, Charmm 27 Lennart Nilsson (Fri May 27 2016 - 15:28:43 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 JC Gumbart (Mon May 30 2016 - 07:19:44 CDT)
- Re: No parameter for ribose ring, Charmm 27 Benjamin Hill (Fri May 27 2016 - 05:51:40 CDT)
- Re: No parameter for ribose ring, Charmm 27 JC Gumbart (Thu May 26 2016 - 18:42:52 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)
- 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)
- I cannot make MD simulation constant in pressure Faramarz Joodaki (Mon May 23 2016 - 14:41:54 CDT)
- Re: I cannot make MD simulation constant in pressure Jeff Comer (Mon May 23 2016 - 16:06:17 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 Peter Freddolino (Mon May 23 2016 - 21:01:23 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 - 22:56:48 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)
- namd leaves zombie processes on nodes? JC Gumbart (Mon May 23 2016 - 10:01:45 CDT)
- firstTimestep error message Laura Joana (Mon May 23 2016 - 05:55:51 CDT)
- SMD simulation problem Shambo Hore (Sun May 22 2016 - 10:37:52 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)
- Adsorption energy of protein in vacuum Madhulika Gupta (Fri May 20 2016 - 06:01:05 CDT)
- Restart multiple walker ABF Atanu Maity (Thu May 19 2016 - 03:32:24 CDT)
- TIP4P water with flexible bonds Hartling, Kathryn (Wed May 18 2016 - 14:32:24 CDT)
- Colvars: Unable to restrict rotation and translation along y and z axes Sourav Ray (Wed May 18 2016 - 07:22:00 CDT)
- MDFF with two symmetry groups Benjamin.Haberl_at_physik.uni-muenchen.de (Tue May 17 2016 - 14:48:19 CDT)
- Error associated with protected variable initialization: Nightly Build version Sourav Ray (Tue May 17 2016 - 13:50:54 CDT)
- Postdoc position available Ivaylo Nikolaev Ivanov (Tue May 17 2016 - 10:05:18 CDT)
- ffTK fitting dihedrals Seth Axen (Tue May 17 2016 - 01:36:02 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)
- Re: Excessively high dE_avg values in FEP output (NAMD CVS) Giacomo Fiorin (Mon May 16 2016 - 18:51:55 CDT)
- Re: Excessively high dE_avg values in FEP output (NAMD CVS) Reza Salari (Tue May 17 2016 - 14:20:32 CDT)
- Re: Excessively high dE_avg values in FEP output (NAMD CVS) Jérôme Hénin (Tue May 17 2016 - 14:44:52 CDT)
- Re: Excessively high dE_avg values in FEP output (NAMD CVS) Brian Radak (Wed May 18 2016 - 13:25:44 CDT)
- Re: Excessively high dE_avg values in FEP output (NAMD CVS) Reza Salari (Thu May 19 2016 - 16:21:08 CDT)
- Re: Excessively high dE_avg values in FEP output (NAMD CVS) Brian Radak (Fri May 20 2016 - 07:47:33 CDT)
- Re: Excessively high dE_avg values in FEP output (NAMD CVS) Jérôme Hénin (Fri May 20 2016 - 10:25:03 CDT)
- RE: Excessively high dE_avg values in FEP output (NAMD CVS) Radak, Brian K (Fri May 20 2016 - 11:58:43 CDT)
- Re: Excessively high dE_avg values in FEP output (NAMD CVS) Reza Salari (Tue May 17 2016 - 14:20:32 CDT)
- Re: Excessively high dE_avg values in FEP output (NAMD CVS) Giacomo Fiorin (Mon May 16 2016 - 18:51:55 CDT)
- Combining Drude structures Jeff Comer (Mon May 16 2016 - 16:25:32 CDT)
- Excessively high dE_avg values in FEP output (NAMD CVS) Reza Salari (Mon May 16 2016 - 12:42:27 CDT)
- Particle Mesh Ewald with Martini Sourav Ray (Mon May 16 2016 - 10:55:14 CDT)
- Some questions on the Deca-Alanine ABF tutorial sunyeping (Mon May 16 2016 - 04:19:33 CDT)
- Re: Some questions on the Deca-Alanine ABF tutorial Jérôme Hénin (Tue May 17 2016 - 10:33:03 CDT)
- Re: Some questions on the Deca-Alanine ABF tutorial sunyeping (Wed May 18 2016 - 03:06:08 CDT)
- Re: Some questions on the Deca-Alanine ABF tutorial sunyeping (Wed May 18 2016 - 20:29:46 CDT)
- Re: Some questions on the Deca-Alanine ABF tutorial sunyeping (Thu May 19 2016 - 22:41:05 CDT)
- Re: Some questions on the Deca-Alanine ABF tutorial Jérôme Hénin (Fri May 20 2016 - 08:07:03 CDT)
- Re: Some questions on the Deca-Alanine ABF tutorial Jérôme Hénin (Tue May 17 2016 - 10:33:03 CDT)
- CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Mon May 16 2016 - 02:45:55 CDT)
- Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Mon May 16 2016 - 04:30:29 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 - 08:54:31 CDT)
- Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params JC Gumbart (Tue May 17 2016 - 09:29:52 CDT)
- Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Francesco Pietra (Tue May 17 2016 - 11:43:05 CDT)
- Re: Re: vmd-l: CHARMM36 alleged missing CC CT1 NH2 angle params Pardis Tabaee (Fri May 20 2016 - 11:12:24 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 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)
- Equilibration and production run dhirajks_at_gmail.com (Mon May 16 2016 - 01:25:32 CDT)
- Coarse-grained simulation with Polarizable Water crashing Sourav Ray (Sun May 15 2016 - 16:34:18 CDT)
- Re: Coarse-grained simulation with Polarizable Water crashing Sourav Ray (Sun May 15 2016 - 17:08:31 CDT)
- Re: Coarse-grained simulation with Polarizable Water crashing Jeff Comer (Mon May 16 2016 - 12:04:43 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)
- PMF calculation using ABF Souvik Sinha (Tue May 10 2016 - 08:57:52 CDT)
- PMEProcessors setting on one node dhirajks_at_gmail.com (Sun May 08 2016 - 21:22:54 CDT)
- gradual heating problem Dhiraj Srivastava (Sun May 08 2016 - 10:27:39 CDT)
- (no subject) Srijita Paul (Sat May 07 2016 - 06:17:48 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)
- 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)
- parameterizing a new solvent faride badalkhani (Tue May 03 2016 - 08:54:06 CDT)
- TCL Scripting for Force Calculations Allen, Caley R (Mon May 02 2016 - 10:48:56 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)
- Dihedral missing faride badalkhani (Thu Apr 28 2016 - 17:54:15 CDT)
- restart file - langevin options removed? Olya Kravchenko (Thu Apr 28 2016 - 14:49:45 CDT)
- Re: restart file - langevin options removed? Maxim Belkin (Thu Apr 28 2016 - 15:00:57 CDT)
- Re: restart file - langevin options removed? Olya Kravchenko (Thu Apr 28 2016 - 15:13:00 CDT)
- Re: restart file - langevin options removed? Josh Vermaas (Thu Apr 28 2016 - 15:16:41 CDT)
- Re: restart file - langevin options removed? Maxim Belkin (Thu Apr 28 2016 - 15:17:35 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 - 15:36:52 CDT)
- Re: restart file - langevin options removed? Olya Kravchenko (Thu Apr 28 2016 - 15:59:09 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)
- minimization, heating, equilibration and production run in one script Dhiraj Srivastava (Thu Apr 28 2016 - 10:05:55 CDT)
- Running a test simulation using GPU only (without any CPU core) Sourav Ray (Thu Apr 28 2016 - 09:40:00 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)
- CHARMM36 and TIP3 Dhiraj Srivastava (Tue Apr 26 2016 - 13:37:49 CDT)
- Amino acid as ligand Dhiraj Srivastava (Mon Apr 25 2016 - 12:22:24 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)
- Re: Constraint failure in RATTLE algorithm for atom 6! Jeff Comer (Tue Apr 26 2016 - 16:14:50 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! Radak, Brian K (Tue Apr 26 2016 - 16:26:30 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 - 16:40:45 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! 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 - 16:22:02 CDT)
- Re: Constraint failure in RATTLE algorithm for atom 6! Jeff Comer (Tue Apr 26 2016 - 16:14:50 CDT)
- XPLOR format PSF file for small molecules Felix W.-H. Weng (Sun Apr 24 2016 - 11:21:45 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)
- 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: Replica exchange arpita agarwal (Fri Apr 22 2016 - 02:54:50 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)
- cell basis vectors faride badalkhani (Wed Apr 20 2016 - 13:59:11 CDT)
- rotation angle giulia palermo (Wed Apr 20 2016 - 12:25:16 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)
- 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)
- ERROR: ofstream_namd::close() called when file is not open Souvik Sinha (Mon Apr 18 2016 - 02:36:33 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)
- Bad initial structure? faride badalkhani (Thu Apr 14 2016 - 13:50:14 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)
- Dynamics of an interface Water/Hexane Jean-François Fabre (Wed Apr 13 2016 - 07:54:17 CDT)
- (no subject) Srijita Paul (Wed Apr 13 2016 - 07:08:28 CDT)
- Polymer moves to the edge of water box during the simulation faride badalkhani (Tue Apr 12 2016 - 16:49:21 CDT)
- Re: Polymer moves to the edge of water box during the simulation Josh Vermaas (Tue Apr 12 2016 - 16:54:35 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 (Wed Apr 13 2016 - 08:02:36 CDT)
- Re: Polymer moves to the edge of water box during the simulation faride badalkhani (Wed Apr 13 2016 - 08:32:29 CDT)
- Re: Polymer moves to the edge of water box during the simulation faride badalkhani (Wed Apr 13 2016 - 12:55:28 CDT)
- Re: Polymer moves to the edge of water box during the simulation faride badalkhani (Thu Apr 14 2016 - 09:56:07 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)
- Unexpected(?) callback behavior when minimizing before MD Radak, Brian K (Tue Apr 12 2016 - 16:02:34 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)
- Ru surface potential Madhulika Gupta (Mon Apr 11 2016 - 03:52:26 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)
- (no subject) Srijita Paul (Fri Apr 08 2016 - 08:00:25 CDT)
- LJ Parameters for Au and S and harmonic constraints Madhulika Gupta (Fri Apr 08 2016 - 02:18:29 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)
- 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)
- FEP/REMD with NAMD2.11 - missing alchLambda? Nathan Lim (Wed Apr 06 2016 - 20:42:58 CDT)
- water box has a weird shape faride badalkhani (Wed Apr 06 2016 - 13:21:28 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)
- Post Doctoral Fellow Opening at IBM for Biomolecular Modeling Tien Huynh (Tue Apr 05 2016 - 18:30:43 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: Constraint failure in RATTLE algorithm for atom 538 Brian Radak (Tue Apr 05 2016 - 10:04:40 CDT)
- Re: Constraint failure in RATTLE algorithm for atom 538 Chitrak Gupta (Tue Apr 05 2016 - 10:10:44 CDT)
- problem with +devices using nikolaev_at_spbau.ru (Tue Apr 05 2016 - 06:35:23 CDT)
- why does the transition seem to be irreversible in aMD sunyeping (Mon Apr 04 2016 - 22:21:00 CDT)
- AW: why does the transition seem to be irreversible in aMD Norman Geist (Tue Apr 05 2016 - 02:29:42 CDT)
- Re: AW: why does the transition seem to be irreversible in aMD sunyeping (Tue Apr 05 2016 - 02:47:39 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: AW: why does the transition seem to be irreversible in aMD sunyeping (Tue Apr 05 2016 - 04:10:59 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: AW: why does the transition seem to be irreversible in aMD Brian Radak (Tue Apr 05 2016 - 09:42:27 CDT)
- Re: AW: AW: AW: why does the transition seem to be irreversible in aMD sunyeping (Mon May 23 2016 - 03:53:37 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)
- 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: 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: 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)
- Dihedral parameter missing faride badalkhani (Mon Apr 04 2016 - 16:26:03 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)
- Stray PME grid charges detected faride badalkhani (Sun Apr 03 2016 - 12:49:18 CDT)
- Running multi-node jobs on Sun Grid Engine Sourav Ray (Sun Apr 03 2016 - 10:49:30 CDT)
- Steered MD diminishing distances giulia palermo (Sat Apr 02 2016 - 20:29:14 CDT)
- maximum coordinate is negative for z faride badalkhani (Fri Apr 01 2016 - 12:14:17 CDT)
- Occasional performance slow down using NAMD with Xeon Phi Mattia Felice Palermo (Fri Apr 01 2016 - 09:53:37 CDT)
- Making NAMD aware of Tcl packages? Brian Radak (Thu Mar 31 2016 - 10:11:07 CDT)
- constant velocity pulling Jamal Zanjani (Thu Mar 31 2016 - 06:04:18 CDT)
- segmentation fault (core dumped) faride badalkhani (Wed Mar 30 2016 - 16:24:26 CDT)
- "Jump" in Energy and Volume graphs of my MD Daniela Rivas (Wed Mar 30 2016 - 15:04:07 CDT)
- Re: "Jump" in Energy and Volume graphs of my MD Peter Freddolino (Wed Mar 30 2016 - 15:23:46 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 - 19:33:49 CDT)
- AW: "Jump" in Energy and Volume graphs of my MD Norman Geist (Thu Mar 31 2016 - 01:00:46 CDT)
- Re: AW: "Jump" in Energy and Volume graphs of my MD Brian Radak (Thu Mar 31 2016 - 07:56:32 CDT)
- Re: AW: "Jump" in Energy and Volume graphs of my MD Jeff Comer (Thu Mar 31 2016 - 08:44:50 CDT)
- Re: "Jump" in Energy and Volume graphs of my MD Peter Freddolino (Thu Mar 31 2016 - 09:13:46 CDT)
- Re: "Jump" in Energy and Volume graphs of my MD Daniela Rivas (Thu Mar 31 2016 - 11:21:03 CDT)
- Re: "Jump" in Energy and Volume graphs of my MD David Hardy (Fri Apr 01 2016 - 12:09:44 CDT)
- Re: "Jump" in Energy and Volume graphs of my MD Peter Freddolino (Wed Mar 30 2016 - 15:23:46 CDT)
- problem with angle parameters faride badalkhani (Wed Mar 30 2016 - 09:01:20 CDT)
- size of water box and cellbasisvectors faride badalkhani (Wed Mar 30 2016 - 07:51:14 CDT)
- Mixing all_36_cgenff with all_36_prot Francesco Pietra (Sat Mar 26 2016 - 13:02:27 CDT)
- HBB2-pol R. Charbel MAROUN (Fri Mar 25 2016 - 09:01:46 CDT)
- Opinions on Haptic Feedback Devices with NAMD/VMD Ben Fritch (Fri Mar 25 2016 - 08:37:31 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)
- 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)
- 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)
- GPU configuration suggestions Nikhil Maroli (Tue Mar 22 2016 - 00:52:25 CDT)
- Postdoctoral opening in biomolecular modeling at IBM Payel Das (Mon Mar 21 2016 - 16:38:19 CDT)
- Basic validation of CGenFF faride badalkhani (Mon Mar 21 2016 - 07:31:05 CDT)
- Testing NAMD scalability Éric 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)
- dynamic_cast & runtime type information Éric Germaneau (Fri Mar 18 2016 - 11:46:10 CDT)
- charge group faride badalkhani (Fri Mar 18 2016 - 10:56:42 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 Ljubetič (Wed Mar 16 2016 - 13:08:59 CDT)
- NAMD survey starting Jim Phillips (Tue Mar 15 2016 - 13:34:00 CDT)
- restarting simulation Francesco Pietra (Mon Mar 14 2016 - 09:45:44 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)
- Tcl script for simulated tempering? Radak, Brian K (Fri Mar 11 2016 - 16:12:21 CST)
- AW: Tcl script for simulated tempering? Norman Geist (Tue Mar 15 2016 - 02:53:21 CDT)
- Re: AW: Tcl script for simulated tempering? Brian Radak (Tue Mar 15 2016 - 08:14:11 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? Radak, Brian K (Tue Mar 15 2016 - 13:01:56 CDT)
- AW: AW: Tcl script for simulated tempering? Norman Geist (Wed Mar 16 2016 - 05:10:14 CDT)
- RE: AW: Tcl script for simulated tempering? Radak, Brian K (Wed Mar 16 2016 - 10:17:07 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)
- Urey-Bradley parameters faride badalkhani (Fri Mar 11 2016 - 09:10:39 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)
- problem with bringing down the pressure faride badalkhani (Thu Mar 10 2016 - 11:31:36 CST)
- periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Wed Mar 09 2016 - 21:23:05 CST)
- AW: periodic boundary condition in XY, hard wall in Z - errors Norman Geist (Thu Mar 10 2016 - 01:05:33 CST)
- Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Thu Mar 10 2016 - 11:21:00 CST)
- Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Thu Mar 10 2016 - 15:58:45 CST)
- Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Thu Mar 10 2016 - 20:01:12 CST)
- Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Fri Mar 11 2016 - 14:34:35 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 - 15:31:50 CST)
- Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Fri Mar 11 2016 - 21:42:23 CST)
- Re: periodic boundary condition in XY, hard wall in Z - errors Maxim Belkin (Mon Mar 14 2016 - 11:24:35 CDT)
- Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Tue Mar 15 2016 - 14:48:58 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 Maxim Belkin (Fri Mar 11 2016 - 14:39:06 CST)
- Re: periodic boundary condition in XY, hard wall in Z - errors Olya Kravchenko (Thu Mar 10 2016 - 11:21:00 CST)
- AW: periodic boundary condition in XY, hard wall in Z - errors Norman Geist (Thu Mar 10 2016 - 01:05:33 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)
- 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: Tutorial example of replica exchange Norman Geist (Thu Mar 10 2016 - 02:03:38 CST)
- Re: Tutorial example of replica exchange Dr. Eddie (Thu Mar 10 2016 - 09:46:50 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 - 12:26:19 CST)
- AW: Tutorial example of replica exchange Norman Geist (Thu Mar 10 2016 - 16:53:22 CST)
- Re: Tutorial example of replica exchange Dr. Eddie (Fri Mar 11 2016 - 09:35:03 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)
- selection error in forces script Olya Kravchenko (Mon Mar 07 2016 - 23:02:34 CST)
- segmentation error Stefano Guglielmo (Fri Mar 04 2016 - 04:15:01 CST)
- applying constant force only within certain part of simulation cell? Olya Kravchenko (Thu Mar 03 2016 - 14:00:33 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)
- 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)
- plumed Stefano Guglielmo (Sun Feb 28 2016 - 10:21:32 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)
- 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)
- AW: Energy increase with fixed atoms in POPC membrane Norman Geist (Fri Feb 19 2016 - 01:47:51 CST)
- external HPC resource Deng, Jinxia (Nancy) (Thu Feb 18 2016 - 10:23:36 CST)
- Should you cap C and N termini? ashika torikora (Thu Feb 18 2016 - 07:09:10 CST)
- Energy increase with fixed atoms in POPC membrane Mihaela Drenscko (Wed Feb 17 2016 - 16:27:15 CST)
- AW: vmd-l: moving atoms and updating distances Norman Geist (Mon Feb 15 2016 - 00:11:47 CST)
- Replica Exchange US, Colvar suggestion Abhishek TYAGI (Sat Feb 13 2016 - 01:07:38 CST)
- Non respect of sequence of commands in command file R. Charbel MAROUN (Fri Feb 12 2016 - 05:11:39 CST)
- velocity computation Patrick Welche (Fri Feb 05 2016 - 13:05:25 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)
- Lennard-Jones potential in coarse grained MD Yongcheng Zhou (Sat Jan 30 2016 - 00:36:20 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)
- PBC in lipid bilayer: receptor vs. ligand R. Charbel MAROUN (Wed Jan 27 2016 - 07:54:34 CST)
- Re: PBC in lipid bilayer: receptor vs. ligand Ajasja Ljubetič (Wed Jan 27 2016 - 09:21:11 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 R. Charbel MAROUN (Thu Jan 28 2016 - 05:26:33 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 - 11:03:17 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 - 11:59:14 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 (Mon Feb 01 2016 - 10:39:06 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)
- (no subject) Srijita Paul (Tue Jan 26 2016 - 23:06:12 CST)
- (no subject) Srijita Paul (Tue Jan 26 2016 - 23:02:28 CST)
- segmentation fault in ABF simulations Azadeh Alavi (Mon Jan 25 2016 - 07:58:49 CST)
- Re: segmentation fault in ABF simulations Jérôme Hénin (Mon Jan 25 2016 - 08:14:47 CST)
- Re: segmentation fault in ABF simulations Azadeh Alavi (Mon Jan 25 2016 - 11:00:26 CST)
- Re: segmentation fault in ABF simulations Jérôme Hénin (Mon Jan 25 2016 - 11:08:22 CST)
- Re: segmentation fault in ABF simulations Azadeh Alavi (Mon Jan 25 2016 - 12:11:58 CST)
- Re: segmentation fault in ABF simulations Jérôme Hénin (Mon Jan 25 2016 - 12:23:01 CST)
- Re: segmentation fault in ABF simulations Azadeh Alavi (Mon Jan 25 2016 - 12:31:10 CST)
- Re: segmentation fault in ABF simulations Jérôme Hénin (Mon Jan 25 2016 - 12:47:00 CST)
- Re: segmentation fault in ABF simulations Azadeh Alavi (Mon Jan 25 2016 - 11:00:26 CST)
- Re: segmentation fault in ABF simulations Jérôme Hénin (Mon Jan 25 2016 - 08:14:47 CST)
- AW: PBC BUG in coorfile + pair interaction Norman Geist (Mon Jan 25 2016 - 02:33:18 CST)
- calculating replica exchange acceptance ratio Chitrak Gupta (Sun Jan 24 2016 - 23:16:09 CST)
- AW: calculating replica exchange acceptance ratio Norman Geist (Mon Jan 25 2016 - 01:13:51 CST)
- Re: calculating replica exchange acceptance ratio Chitrak Gupta (Mon Jan 25 2016 - 02:54:15 CST)
- AW: calculating replica exchange acceptance ratio Norman Geist (Mon Jan 25 2016 - 04:37:56 CST)
- AW: calculating replica exchange acceptance ratio Norman Geist (Mon Jan 25 2016 - 05:51:31 CST)
- Re: calculating replica exchange acceptance ratio Chitrak Gupta (Mon Jan 25 2016 - 09:51:48 CST)
- Re: calculating replica exchange acceptance ratio Chitrak Gupta (Mon Jan 25 2016 - 09:58:31 CST)
- AW: calculating replica exchange acceptance ratio Norman Geist (Tue Jan 26 2016 - 08:03:40 CST)
- Re: calculating replica exchange acceptance ratio Chitrak Gupta (Wed Jan 27 2016 - 04:18:38 CST)
- Re: calculating replica exchange acceptance ratio Chitrak Gupta (Mon Jan 25 2016 - 02:54:15 CST)
- AW: calculating replica exchange acceptance ratio Norman Geist (Mon Jan 25 2016 - 01:13:51 CST)
- compute capability Stefano Guglielmo (Sun Jan 24 2016 - 17:15:43 CST)
- charmc rpath Scott Brozell (Thu Jan 21 2016 - 22:04:41 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)
- Re: Enabling GPU for Replica exchange umbrella sampling Abhishek TYAGI (Thu Jan 21 2016 - 22:02:59 CST)
- AW: Re: Enabling GPU for Replica exchange umbrella sampling Norman Geist (Fri Jan 22 2016 - 03:07:59 CST)
- AW: Enabling GPU for Replica exchange umbrella sampling Norman Geist (Fri Jan 22 2016 - 03:09:24 CST)
- Re: Enabling GPU for Replica exchange umbrella sampling Abhishek TYAGI (Mon Jan 25 2016 - 01:49:23 CST)
- Re: Enabling GPU for Replica exchange umbrella sampling Abhishek TYAGI (Thu Jan 21 2016 - 22:02:59 CST)
- multipld .dcd analysis by VMD Deng, Jinxia (Nancy) (Wed Jan 20 2016 - 13:53:21 CST)
- LSU SuperMIC Jeff Comer (Tue Jan 19 2016 - 16:21:39 CST)
- Replica Exchange Dr. Eddie (Tue Jan 19 2016 - 10:35:00 CST)
- about User-Defined Forces ߾ (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)
- 2.11 how to remove charmrun remote-shell options Scott Brozell (Wed Jan 13 2016 - 12:04:54 CST)
- restart namd calculations Bylund, Tatsiana (NIH/NIAID) [F] (Tue Jan 12 2016 - 16:55:09 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)
- AW: Compilation error across Intel 14,15 and 16 (UNCLASSIFIED) Norman Geist (Tue Jan 12 2016 - 02:16:38 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)
- 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 - 09:44:54 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 - 14:04:36 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)
- AW: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Norman Geist (Wed Jan 13 2016 - 02:17:01 CST)
- RE: Compilation error across Intel 14,15 and 16 (UNCLASSIFIED) Tim.Ho_at_csiro.au (Wed Jan 13 2016 - 22:28:53 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)
- AW: Compilation error across Intel 14,15 and 16 (UNCLASSIFIED) Norman Geist (Tue Jan 12 2016 - 02:16:38 CST)
- Fwd: Regarding system forces in NAMD sruthi c k (Fri Jan 08 2016 - 03:38:26 CST)
- TIP4P/2005 par file by Jordi Faraudo Monika Madhavi (Sat Jan 09 2016 - 07:16:17 CST)
- PhD and postdoctoral positions in biomolecular simulation Allison, Jane (Thu Jan 07 2016 - 19:01:29 CST)
- Regarding system forces in NAMD sruthi c k (Thu Jan 07 2016 - 06:49:51 CST)
- Re: Regarding system forces in NAMD Jérôme Hénin (Thu Jan 07 2016 - 08:37:07 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)
- solvent other than water Deng, Jinxia (Nancy) (Wed Jan 06 2016 - 12:17:11 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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