NAMD-L: By Date

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NAMD-L: By Date

By Date

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About this archive

Starting: Mon Jan 01 2018 - 09:14:56 CST
Ending: Mon Dec 30 2019 - 20:12:28 CST

Support of recent Amber force field Haohao Fu (Mon Dec 30 2019 - 20:11:54 CST)
Antw: Re: slow down when running 2 simulations on 1 node Gerald Keller (Sun Dec 29 2019 - 07:29:48 CST)
Re: slow down when running 2 simulations on 1 node Miro Astore (Fri Dec 27 2019 - 16:42:25 CST)
Re: slow down when running 2 simulations on 1 node Bryan Roessler (Fri Dec 27 2019 - 11:58:06 CST)
AW: slow down when running 2 simulations on 1 node Norman Geist (Wed Dec 18 2019 - 06:06:18 CST)
Re: slow down when running 2 simulations on 1 node Gerald Keller (Wed Dec 18 2019 - 05:33:21 CST)
Cuda Geordano Palacios (Tue Dec 17 2019 - 11:59:56 CST)
Re: slow down when running 2 simulations on 1 node David Hardy (Mon Dec 16 2019 - 12:36:12 CST)
Gradual minimization Geordano Palacios (Sat Dec 14 2019 - 10:00:16 CST)
Re: slow down when running 2 simulations on 1 node Gerald Keller (Sat Dec 14 2019 - 09:51:09 CST)
Ion concentration and aggregation problem of the nuclear protein simulations kilincc18_at_itu.edu.tr (Fri Dec 13 2019 - 09:19:07 CST)
Re: Protein:ligand standard binding free energies Abhijit Gogoi (Fri Dec 13 2019 - 10:51:27 CST)
Re: slow down when running 2 simulations on 1 node Giacomo Fiorin (Thu Dec 12 2019 - 13:26:28 CST)
Re: slow down when running 2 simulations on 1 node Julio Maia (Thu Dec 12 2019 - 13:13:01 CST)
Re: slow down when running 2 simulations on 1 node Henrik Schopmans (Thu Dec 12 2019 - 12:58:26 CST)
Re: fatal error regarding parameters mohammad goodarzi (Thu Dec 12 2019 - 09:55:08 CST)
Re: slow down when running 2 simulations on 1 node Victor Kwan (Thu Dec 12 2019 - 08:03:10 CST)
Re: slow down when running 2 simulations on 1 node Gerald Keller (Thu Dec 12 2019 - 05:18:47 CST)
Re: slow down when running 2 simulations on 1 node Miro Astore (Thu Dec 12 2019 - 04:10:05 CST)
Re: Protein:ligand standard binding free energies SHIVAM TIWARI (Thu Dec 12 2019 - 03:50:46 CST)
Re: fatal error regarding parameters Adupa Vasista (Thu Dec 12 2019 - 02:40:47 CST)
slow down when running 2 simulations on 1 node Gerald Keller (Thu Dec 12 2019 - 02:09:14 CST)
RE: Protein:ligand standard binding free energies Sanjay Hari (Wed Dec 11 2019 - 13:29:49 CST)
Re: Protein:ligand standard binding free energies mohammad goodarzi (Wed Dec 11 2019 - 12:37:52 CST)
Re: Protein:ligand standard binding free energies mohammad goodarzi (Wed Dec 11 2019 - 12:33:15 CST)
RE: fatal error regarding parameters Vermaas, Joshua (Wed Dec 11 2019 - 12:28:56 CST)
Re: Protein:ligand standard binding free energies Joao Ribeiro (Wed Dec 11 2019 - 11:37:58 CST)
Re: Protein:ligand standard binding free energies Chris Chipot (Wed Dec 11 2019 - 11:28:37 CST)
Re: fatal error regarding parameters mohammad goodarzi (Wed Dec 11 2019 - 11:22:15 CST)
Protein:ligand standard binding free energies mohammad goodarzi (Wed Dec 11 2019 - 11:12:13 CST)
Re: fatal error regarding parameters Adupa Vasista (Wed Dec 11 2019 - 01:51:15 CST)
RE: fatal error regarding parameters Vermaas, Joshua (Tue Dec 10 2019 - 18:09:24 CST)
Re: fatal error regarding parameters Chandni Tiwari (Tue Dec 10 2019 - 17:55:12 CST)
Re: fatal error regarding parameters mohammad goodarzi (Tue Dec 10 2019 - 12:15:01 CST)
Re: Running multiple walker metadynamics on Stampede2 Giacomo Fiorin (Tue Dec 10 2019 - 12:01:12 CST)
Re: fatal error regarding parameters Adupa Vasista (Tue Dec 10 2019 - 11:28:22 CST)
fatal error regarding parameters mohammad goodarzi (Tue Dec 10 2019 - 11:04:21 CST)
Regarding PCA SHOBHIT JAIN . (Mon Dec 09 2019 - 23:51:00 CST)
Re: vivek nani (Thu Dec 05 2019 - 10:17:12 CST)
Re: Gustavo Olivos (Thu Dec 05 2019 - 09:35:48 CST)
Re: Aravinda Munasinghe (Thu Dec 05 2019 - 09:33:27 CST)
Hybrid AA/CG for a transmembrane protein system Alison de Sousa RebouÃ§as (Thu Dec 05 2019 - 08:58:37 CST)
(no subject) vivek nani (Thu Dec 05 2019 - 03:43:47 CST)
Re: Running multiple walker metadynamics on Stampede2 Sebastian S (Wed Dec 04 2019 - 21:44:38 CST)
Re: gamd restart file in namd 2.13 Aravinda Munasinghe (Wed Dec 04 2019 - 10:54:20 CST)
Re: gamd restart file in namd 2.13 Pang, Yui Tik (Wed Dec 04 2019 - 09:55:30 CST)
Re: Simulation of sodium dodecyl sulfate Mikhail Suyetin (Wed Dec 04 2019 - 09:51:10 CST)
RE: Running multiple walker metadynamics on Stampede2 Vermaas, Joshua (Tue Dec 03 2019 - 11:15:58 CST)
gamd restart file in namd 2.13 Aravinda Munasinghe (Tue Dec 03 2019 - 08:17:20 CST)
Running multiple walker metadynamics on Stampede2 Sebastian S (Mon Dec 02 2019 - 22:43:09 CST)
Re: rigid body simulation with NAMD Jovan Dragelj (Fri Nov 29 2019 - 12:36:07 CST)
Re: rigid body simulation with NAMD Jovan Dragelj (Fri Nov 29 2019 - 02:46:04 CST)
Re: rigid body simulation with NAMD Victor Kwan (Thu Nov 28 2019 - 15:53:27 CST)
rigid body simulation with NAMD Jovan Dragelj (Thu Nov 28 2019 - 15:16:38 CST)
Re: Problem with compiling vmd from source code Victor Kwan (Wed Nov 27 2019 - 11:06:46 CST)
Problem with compiling vmd from source code Oleksii (Wed Nov 27 2019 - 09:29:40 CST)
Re: Colvar orientation of polymer Henrik Schopmans (Wed Nov 27 2019 - 00:48:13 CST)
Re: Multi canonical ensemble method Takeru KAMEDA (Wed Nov 27 2019 - 00:19:06 CST)
Re: Colvar orientation of polymer Giacomo Fiorin (Tue Nov 26 2019 - 13:16:04 CST)
Colvar orientation of polymer Henrik Schopmans (Tue Nov 26 2019 - 12:53:21 CST)
Re: PCA calculations Poonam Pandey (Tue Nov 26 2019 - 10:25:16 CST)
PCA calculations SHOBHIT JAIN . (Sat Nov 23 2019 - 22:02:58 CST)
Re: use Colvars to track four group of pair atoms distance at same time? yjcoshc_at_gmail.com (Fri Nov 22 2019 - 20:42:11 CST)
Re: use Colvars to track four group of pair atoms distance at same time? Jiali Wang (Fri Nov 22 2019 - 19:56:18 CST)
Re: use Colvars to track four group of pair atoms distance at same time? yjcoshc_at_gmail.com (Fri Nov 22 2019 - 13:23:13 CST)
use Colvars to track four group of pair atoms distance at same time? Jiali Wang (Fri Nov 22 2019 - 12:59:32 CST)
Re: NAMD-QM/MM TUTORIAL: Atoms moving too fast error M. A (Fri Nov 22 2019 - 09:43:20 CST)
Re: Job submission error for NAMD-2.13 ( version netlrts with cuda-10.0) using Torque job scheduler Daipayan Sarkar (Tue Nov 19 2019 - 15:19:10 CST)
Re: Job submission error for NAMD-2.13 ( version netlrts with cuda-10.0) using Torque job scheduler Victor Kwan (Tue Nov 19 2019 - 14:57:56 CST)
Job submission error for NAMD-2.13 ( version netlrts with cuda-10.0) using Torque job scheduler Daipayan Sarkar (Tue Nov 19 2019 - 14:49:51 CST)
Re: Error in the collective variables Victor Kwan (Tue Nov 19 2019 - 14:27:41 CST)
Re: Error in the collective variables Giacomo Fiorin (Tue Nov 19 2019 - 14:21:53 CST)
RE: Simulation of sodium dodecyl sulfate Vermaas, Joshua (Tue Nov 19 2019 - 13:12:04 CST)
Error in the collective variables Jiali Wang (Tue Nov 19 2019 - 12:48:25 CST)
Re: Simulation of sodium dodecyl sulfate Giacomo Fiorin (Tue Nov 19 2019 - 11:56:56 CST)
Re: Simulation of sodium dodecyl sulfate Mikhail Suyetin (Tue Nov 19 2019 - 10:56:16 CST)
Re: Doubt about ABF and PMF file generation Souvik Sinha (Mon Nov 18 2019 - 12:52:52 CST)
Re: Doubt about ABF and PMF file generation Souvik Sinha (Mon Nov 18 2019 - 12:26:33 CST)
Re: looping on multiple dcds in namd configuration file SHIVAM TIWARI (Sat Nov 16 2019 - 07:50:38 CST)
Re: How to integrate multiple walkers 2D metadynamics results? Sebastian S (Fri Nov 15 2019 - 18:29:23 CST)
Re: Selected cofactor in final output Giacomo Fiorin (Fri Nov 15 2019 - 13:14:29 CST)
Re: How to integrate multiple walkers 2D metadynamics results? Giacomo Fiorin (Fri Nov 15 2019 - 13:12:00 CST)
Re: How to integrate multiple walkers 2D metadynamics results? Sebastian S (Fri Nov 15 2019 - 12:39:29 CST)
Re: How to integrate multiple walkers 2D metadynamics results? Sebastian S (Fri Nov 15 2019 - 12:34:57 CST)
RE: looping on multiple dcds in namd configuration file Vermaas, Joshua (Fri Nov 15 2019 - 11:26:19 CST)
Re: How to integrate multiple walkers 2D metadynamics results? Canal de Sebassen (Fri Nov 15 2019 - 11:25:34 CST)
Selected cofactor in final output Aashish Bhatt (Fri Nov 15 2019 - 08:47:32 CST)
Re: looping on multiple dcds in namd configuration file SHIVAM TIWARI (Fri Nov 15 2019 - 06:25:46 CST)
Re: looping on multiple dcds in namd configuration file Miro Astore (Fri Nov 15 2019 - 05:22:34 CST)
Re: looping on multiple dcds in namd configuration file SHIVAM TIWARI (Fri Nov 15 2019 - 00:59:51 CST)
Re: looping on multiple dcds in namd configuration file Miro Astore (Fri Nov 15 2019 - 00:44:37 CST)
looping on multiple dcds in namd configuration file SHIVAM TIWARI (Fri Nov 15 2019 - 00:33:23 CST)
Re: Doubt about ABF and PMF file generation Souvik Sinha (Fri Nov 15 2019 - 00:03:11 CST)
RE: Simulation of sodium dodecyl sulfate Vermaas, Joshua (Thu Nov 14 2019 - 10:46:05 CST)
Simulation of sodium dodecyl sulfate Mikhail Suyetin (Thu Nov 14 2019 - 08:00:33 CST)
Doubt about ABF and PMF file generation Ercalary . (Mon Nov 11 2019 - 14:15:55 CST)
Doubt about abf and pmf file generation Constanza Galaz Araya (Mon Nov 11 2019 - 12:41:26 CST)
Re: NAMD-QM/MM TUTORIAL: Atoms moving too fast error Marcelo C. R. Melo (Mon Nov 11 2019 - 09:50:36 CST)
Re: Harmonic restrains Miro Astore (Sun Nov 10 2019 - 22:07:15 CST)
Re: Harmonic restrains Zhang Yan (Sun Nov 10 2019 - 20:42:45 CST)
NAMD-QM/MM TUTORIAL: Atoms moving too fast error M. A (Sun Nov 10 2019 - 03:50:49 CST)
Re: Harmonic restrains Miro Astore (Sat Nov 09 2019 - 19:25:30 CST)
Re: How to integrate multiple walkers 2D metadynamics results? Canal de Sebassen (Sat Nov 09 2019 - 19:03:01 CST)
Re: Harmonic restrains Miro Astore (Sat Nov 09 2019 - 03:17:41 CST)
Re: Harmonic restrains Miro Astore (Sat Nov 09 2019 - 03:08:36 CST)
Harmonic restrains Zhang Yan (Sat Nov 09 2019 - 02:20:49 CST)
Re: Performance on GPU Anup Prasad (Fri Nov 08 2019 - 05:35:37 CST)
Re: How to integrate multiple walkers 2D metadynamics results? Giacomo Fiorin (Thu Nov 07 2019 - 17:37:11 CST)
How to integrate multiple walkers 2D metadynamics results? Canal de Sebassen (Thu Nov 07 2019 - 17:04:15 CST)
Re: Homologous structure as stating flexible fitting model Miro Astore (Wed Nov 06 2019 - 21:09:12 CST)
Re: Homologous structure as stating flexible fitting model Zhang Yan (Wed Nov 06 2019 - 20:39:23 CST)
Re: Multi canonical ensemble method Giacomo Fiorin (Wed Nov 06 2019 - 13:32:45 CST)
RE: Performance on GPU Vermaas, Joshua (Wed Nov 06 2019 - 09:00:41 CST)
Re: Multi canonical ensemble method Takeru KAMEDA (Wed Nov 06 2019 - 03:58:33 CST)
Re: Homologous structure as stating flexible fitting model Miro Astore (Wed Nov 06 2019 - 01:27:56 CST)
Homologous structure as stating flexible fitting model Zhang Yan (Wed Nov 06 2019 - 01:10:55 CST)
Re: Performance on GPU Anup Prasad (Tue Nov 05 2019 - 23:40:27 CST)
flexible fitting for helical structure Zhang Yan (Tue Nov 05 2019 - 20:01:28 CST)
RE: Performance on GPU Vermaas, Joshua (Tue Nov 05 2019 - 11:33:02 CST)
Performance on GPU Anup Prasad (Tue Nov 05 2019 - 07:29:58 CST)
Re: Multi canonical ensemble method Giacomo Fiorin (Tue Nov 05 2019 - 07:18:49 CST)
Re: Differences between z-gradient and gradient in ABF simulation JÃ©rÃ´me HÃ©nin (Mon Nov 04 2019 - 07:12:57 CST)
Re: auto psf file generation Chandni Tiwari (Mon Nov 04 2019 - 03:04:24 CST)
auto psf file generation Zhang Yan (Mon Nov 04 2019 - 02:52:05 CST)
running pair interaction analysis multiple dcds in sequence in single run SHIVAM TIWARI (Fri Nov 01 2019 - 09:59:54 CDT)
FATAL ERROR: FOUND ISOLATED LONE PAIR Nibedita Ray Chaudhuri (Fri Nov 01 2019 - 07:35:49 CDT)
Re: Multi canonical ensemble method Giacomo Fiorin (Wed Oct 30 2019 - 09:22:58 CDT)
Re: Multi canonical ensemble method Takeru KAMEDA (Wed Oct 30 2019 - 00:26:28 CDT)
Re: Should a pairlist warning concern me? Victor Kwan (Mon Oct 28 2019 - 09:35:55 CDT)
Differences between z-gradient and gradient in ABF simulation Surbhi patel (Mon Oct 28 2019 - 06:23:06 CDT)
Should a pairlist warning concern me? Henrik Schopmans (Mon Oct 28 2019 - 05:59:10 CDT)
Re: Need help with errors in REST2 sample file Han, Yuwei (Mon Oct 28 2019 - 02:28:15 CDT)
Re: RE: charmrun error: Work completion error in sendCq Julio Maia (Thu Oct 24 2019 - 16:05:50 CDT)
RE: RE: charmrun error: Work completion error in sendCq Vermaas, Joshua (Thu Oct 24 2019 - 15:40:47 CDT)
Re: RE: charmrun error: Work completion error in sendCq Julio Maia (Thu Oct 24 2019 - 15:30:24 CDT)
RE: charmrun error: Work completion error in sendCq Vermaas, Joshua (Thu Oct 24 2019 - 14:53:53 CDT)
Re: Need help with errors in REST2 sample file Han, Yuwei (Wed Oct 23 2019 - 00:23:49 CDT)
Re: Need help with errors in REST2 sample file Chitrak Gupta (Tue Oct 22 2019 - 22:47:44 CDT)
Re: Need help with errors in REST2 sample file Chandni Tiwari (Tue Oct 22 2019 - 17:47:16 CDT)
Need help with errors in REST2 sample file Han, Yuwei (Mon Oct 21 2019 - 22:28:46 CDT)
RE: charmrun error: Work completion error in sendCq Pang, Yui Tik (Sat Oct 19 2019 - 16:26:33 CDT)
RE: charmrun error: Work completion error in sendCq Vermaas, Joshua (Sat Oct 19 2019 - 15:55:11 CDT)
charmrun error: Work completion error in sendCq Pang, Yui Tik (Sat Oct 19 2019 - 11:10:07 CDT)
RE: ERROR During MPI run Vermaas, Joshua (Tue Oct 15 2019 - 11:13:19 CDT)
Reduce verbosity during minimization Sanjay Hari (Sat Oct 12 2019 - 17:55:04 CDT)
RE: ERROR During MPI run Vermaas, Joshua (Sat Oct 12 2019 - 16:38:24 CDT)
ERROR During MPI run SHOBHIT JAIN . (Sat Oct 12 2019 - 00:18:54 CDT)
Re: Segfault during NAMD compilation with GCC 8.3 fabricio (Thu Oct 10 2019 - 18:18:35 CDT)
Segfault during NAMD compilation with GCC 8.3 Marcelo C. R. Melo (Thu Oct 10 2019 - 17:58:12 CDT)
Re: Error while runing simulation for protein docking SHOBHIT JAIN . (Thu Oct 10 2019 - 01:38:51 CDT)
Re: vmd-l: query on how to allow the protein to interact with the water molecules Joao Ribeiro (Tue Oct 08 2019 - 09:01:51 CDT)
RE: psfgen error protein-ligand Pavel Kostadinov (Tue Oct 08 2019 - 08:17:46 CDT)
RE: psfgen error protein-ligand Vermaas, Joshua (Mon Oct 07 2019 - 10:03:53 CDT)
RE: Error while runing simulation for protein docking Vermaas, Joshua (Mon Oct 07 2019 - 09:50:44 CDT)
Error while runing simulation for protein docking SHOBHIT JAIN . (Sun Oct 06 2019 - 15:01:24 CDT)
Re: psfgen error protein-ligand Pavel Kostadinov (Sat Oct 05 2019 - 11:17:07 CDT)
Re: psfgen error protein-ligand Adupa Vasista (Fri Oct 04 2019 - 10:41:31 CDT)
Re: psfgen error protein-ligand Joao Ribeiro (Fri Oct 04 2019 - 10:29:39 CDT)
Re: Distance restraints Paula Mihaljevic-Juric (Fri Oct 04 2019 - 07:35:59 CDT)
Re: Distance restraints Giacomo Fiorin (Fri Oct 04 2019 - 07:01:46 CDT)
Re: Regarding psf generation SHOBHIT JAIN . (Fri Oct 04 2019 - 07:06:52 CDT)
psfgen error protein-ligand Pavel Kostadinov (Fri Oct 04 2019 - 02:42:08 CDT)
Distance restraints Paula Mihaljevic-Juric (Fri Oct 04 2019 - 02:21:47 CDT)
FATAL ERROR: PBC Raha YS (Thu Oct 03 2019 - 14:20:40 CDT)
Re: namd on AWS Milad Lagzian (Thu Oct 03 2019 - 00:39:20 CDT)
Re: namd on AWS Miro Astore (Wed Oct 02 2019 - 15:47:38 CDT)
RE: namd on AWS Sanjay Hari (Wed Oct 02 2019 - 11:00:55 CDT)
Re: Regarding psf generation Joao Ribeiro (Wed Oct 02 2019 - 10:21:48 CDT)
GBIS parameters Paula Mihaljevic-Juric (Wed Oct 02 2019 - 09:57:40 CDT)
Fwd: namd on AWS Miro Astore (Tue Oct 01 2019 - 22:46:56 CDT)
Re: Regarding psf generation Joao Ribeiro (Tue Oct 01 2019 - 09:10:29 CDT)
Re: namd on AWS Sanjay Hari (Tue Oct 01 2019 - 05:42:15 CDT)
namd on AWS Miro Astore (Tue Oct 01 2019 - 00:02:14 CDT)
Re: Regarding psf generation Joao Ribeiro (Mon Sep 30 2019 - 12:54:46 CDT)
Re: protein movement Giacomo Fiorin (Mon Sep 30 2019 - 07:11:08 CDT)
Doubt in generating Ficoll 70 Hard Sphere for Coarse Grain Simulation SHOBHIT JAIN . (Mon Sep 30 2019 - 07:00:17 CDT)
Re: Regarding Hard sphere Roshan Shrestha (Mon Sep 30 2019 - 02:39:00 CDT)
Regarding psf generation SHOBHIT JAIN . (Mon Sep 30 2019 - 02:39:04 CDT)
Regarding Hard sphere SHOBHIT JAIN . (Mon Sep 30 2019 - 02:34:28 CDT)
Multi canonical ensemble method Takeru KAMEDA (Sun Sep 29 2019 - 21:19:47 CDT)
RE: protein movement Vermaas, Joshua (Sun Sep 29 2019 - 16:32:03 CDT)
protein movement Mahdi Mousaei (Sun Sep 29 2019 - 14:58:30 CDT)
RE: SMwST RATTLE Algorithm Vermaas, Joshua (Wed Sep 25 2019 - 09:42:53 CDT)
Re: parameters and topology for Deacylcortivazol (DAC) Victor Kwan (Wed Sep 25 2019 - 05:23:53 CDT)
parameters and topology for Deacylcortivazol (DAC) Ester 94 (Wed Sep 25 2019 - 03:48:11 CDT)
SMwST RATTLE Algorithm Xander Gonzalez (Tue Sep 24 2019 - 16:28:24 CDT)
Re: vmd-l: Re: Is there someway to render protein picture without background color? John Stone (Thu Sep 19 2019 - 10:13:52 CDT)
MAIL ABOUT INTRODUCING NEW residue Vidhya Sankar (Thu Sep 19 2019 - 08:27:09 CDT)
AW: vmd-l: Re: Is there someway to render protein picture without background color? Norman Geist (Thu Sep 19 2019 - 04:13:05 CDT)
Re: vmd-l: Re: Is there someway to render protein picture without background color? John Stone (Wed Sep 18 2019 - 10:18:52 CDT)
Re: vmd-l: Re: Is there someway to render protein picture without background color? jiali wang (Wed Sep 18 2019 - 10:14:28 CDT)
Re: vmd-l: Re: Is there someway to render protein picture without background color? John Stone (Tue Sep 17 2019 - 16:11:48 CDT)
Accelerated MD with transmembrane protein Alison de Sousa RebouÃ§as (Tue Sep 17 2019 - 13:48:46 CDT)
Re: Barostat dimension rescaling under semi-isotropic pressure coupling conditions Victor Kwan (Mon Sep 16 2019 - 17:24:41 CDT)
Barostat dimension rescaling under semi-isotropic pressure coupling conditions Milka Doktorova (Mon Sep 16 2019 - 16:56:45 CDT)
RE: Amber topology for mutation Vermaas, Joshua (Mon Sep 16 2019 - 13:22:25 CDT)
Re: Amber topology for mutation Victor Kwan (Mon Sep 16 2019 - 12:42:12 CDT)
Amber topology for mutation Aashish Bhatt (Mon Sep 16 2019 - 10:40:50 CDT)
Re: Brian Radak (Sun Sep 15 2019 - 18:00:36 CDT)
(no subject) SHOBHIT JAIN . (Sun Sep 15 2019 - 14:36:29 CDT)
Re: Is there someway to render protein picture without background color? Jiali Wang (Sun Sep 15 2019 - 09:58:40 CDT)
Re: Is there someway to render protein picture without background color? Chandni Tiwari (Sun Sep 15 2019 - 02:16:43 CDT)
Re: Is there someway to render protein picture without background color? Roshan Shrestha (Sat Sep 14 2019 - 23:44:28 CDT)
Re: Is there someway to render protein picture without background color? Jiali Wang (Sat Sep 14 2019 - 21:19:50 CDT)
Re: Is there someway to render protein picture without background color? Chitrak Gupta (Sat Sep 14 2019 - 20:52:08 CDT)
Is there someway to render protein picture without background color? jiali wang (Sat Sep 14 2019 - 20:25:54 CDT)
Heating problem for protein/ligand complex Alessandro Ruda (Fri Sep 13 2019 - 13:31:56 CDT)
Re: Pulling only one half of a harmonic restraint Miro Astore (Fri Sep 13 2019 - 04:26:13 CDT)
Pulling only one half of a harmonic restraint Miro Astore (Fri Sep 13 2019 - 03:02:44 CDT)
Re: Salvation of non-orthogonal box HEMANTH H 18310019 (Thu Sep 12 2019 - 21:38:40 CDT)
Salvation of non-orthogonal box Yousefi, Raziyeh (Thu Sep 12 2019 - 13:43:56 CDT)
Regarding FICOLL 70 & PEG20000 SHOBHIT JAIN . (Thu Sep 12 2019 - 05:55:53 CDT)
Re: veccross implementation in tclforces Victor Kwan (Wed Sep 11 2019 - 17:59:58 CDT)
Re: veccross implementation in tclforces Victor Kwan (Wed Sep 11 2019 - 17:48:49 CDT)
veccross implementation in tclforces Daniel Strahs (Wed Sep 11 2019 - 16:55:53 CDT)
Periodic boundary condition Weitao Wang (Wed Sep 11 2019 - 16:08:05 CDT)
Re: Regarding number of water molecule Srijita Paul (Tue Sep 10 2019 - 01:19:07 CDT)
Regarding number of water molecule SHOBHIT JAIN . (Tue Sep 10 2019 - 01:14:45 CDT)
Re: Running NAMD on Amazon AMI Ryan McGreevy (Wed Sep 04 2019 - 13:22:04 CDT)
Running NAMD on Amazon AMI Sanjay Hari (Wed Sep 04 2019 - 13:05:12 CDT)
RE: Namd Vermaas, Joshua (Tue Sep 03 2019 - 09:49:40 CDT)
Namd Joey Gehring (Mon Sep 02 2019 - 20:35:08 CDT)
Re: RDF of hydroxide ion in a water box Haohao Fu (Mon Sep 02 2019 - 01:19:31 CDT)
Protein Deformity in Implicit Solvent Simulation Athena Xue (Sun Sep 01 2019 - 18:46:48 CDT)
RE: Fwd: running NAMD with AMBER inputs Vermaas, Joshua (Sun Sep 01 2019 - 14:50:36 CDT)
Re: RDF of hydroxide ion in a water box RonitS Chem (Sun Sep 01 2019 - 14:10:43 CDT)
Fwd: running NAMD with AMBER inputs Rui Chen (Sun Sep 01 2019 - 13:13:12 CDT)
Re: nan (Not a number) error in meta-eABF simulation Dhiman Ray (Sun Sep 01 2019 - 03:11:02 CDT)
Re: nan (Not a number) error in meta-eABF simulation Haohao Fu (Sun Sep 01 2019 - 01:18:03 CDT)
nan (Not a number) error in meta-eABF simulation Dhiman Ray (Sat Aug 31 2019 - 22:00:39 CDT)
Re: Thermodynamic Integration document Brian Radak (Sat Aug 31 2019 - 14:32:38 CDT)
Thermodynamic Integration document Aashish Bhatt (Sat Aug 31 2019 - 04:26:30 CDT)
Re: NAMD configuration file Victor Kwan (Thu Aug 29 2019 - 19:52:03 CDT)
Re: NAMD configuration file Rui Chen (Thu Aug 29 2019 - 19:32:43 CDT)
Re: Hamiltonian Replica exchange configuration file neha rana (Thu Aug 29 2019 - 18:18:09 CDT)
RE: Hamiltonian Replica exchange configuration file Vermaas, Joshua (Thu Aug 29 2019 - 17:47:54 CDT)
Hamiltonian Replica exchange configuration file neha rana (Thu Aug 29 2019 - 15:57:50 CDT)
NAMD configuration file Rui Chen (Tue Aug 27 2019 - 15:54:59 CDT)
Re: pairlist question Jiali Wang (Mon Aug 26 2019 - 10:41:02 CDT)
Postdoctoral researcher position in computational virology. Juan R. Perilla (Mon Aug 26 2019 - 10:37:58 CDT)
pairlist question Rui Chen (Mon Aug 26 2019 - 10:26:27 CDT)
heating Rui Chen (Sat Aug 24 2019 - 11:16:21 CDT)
RDF of hydroxide ion in a water box RonitS Chem (Thu Aug 22 2019 - 21:15:18 CDT)
SMD for understanding the proximity of two atoms Roshan Shrestha (Wed Aug 21 2019 - 10:47:01 CDT)
Re: Can't set multiple harmonic restrains in colvar module Lucas Neumann (Wed Aug 21 2019 - 09:18:39 CDT)
Re: DNA won't translocate through graphene nanopore Canal de Sebassen (Tue Aug 20 2019 - 23:37:50 CDT)
Re: DNA won't translocate through graphene nanopore Mohsen Farshad (Tue Aug 20 2019 - 20:54:21 CDT)
Re: DNA won't translocate through graphene nanopore Priyanka Mondal (Tue Aug 20 2019 - 20:02:50 CDT)
Re: DNA won't translocate through graphene nanopore Canal de Sebassen (Tue Aug 20 2019 - 19:43:37 CDT)
RE: question about SMD Vermaas, Joshua (Tue Aug 20 2019 - 14:55:31 CDT)
question about SMD Maria Bykhovskaia (Tue Aug 20 2019 - 14:44:32 CDT)
DNA won't translocate through graphene nanopore Priyanka Mondal (Tue Aug 20 2019 - 14:04:52 CDT)
Re: Mailing list for Postdoctoral opportunities in Simulations Karteek Bejagam (Tue Aug 20 2019 - 01:36:20 CDT)
Mailing list for Postdoctoral opportunities in Simulations Peter Mawanga (Tue Aug 20 2019 - 01:24:38 CDT)
Re: Can't set multiple harmonic restrains in colvar module Victor Kwan (Mon Aug 19 2019 - 15:06:23 CDT)
RE: Can't set multiple harmonic restrains in colvar module Vermaas, Joshua (Mon Aug 19 2019 - 13:37:46 CDT)
Can't set multiple harmonic restrains in colvar module Lucas Neumann (Mon Aug 19 2019 - 12:44:28 CDT)
Re: AMBER force field parameters Victor Kwan (Fri Aug 16 2019 - 16:35:12 CDT)
Swarms Errors Xander Gonzalez (Fri Aug 16 2019 - 13:10:45 CDT)
(no subject) vivek nani (Fri Aug 16 2019 - 02:01:18 CDT)
Re: REST and Periodic Cell Issues Jeff Comer (Thu Aug 15 2019 - 17:04:22 CDT)
Re: REST and Periodic Cell Issues Giacomo Fiorin (Thu Aug 15 2019 - 08:53:14 CDT)
Re: REST and Periodic Cell Issues Gumbart, JC (Thu Aug 15 2019 - 08:39:56 CDT)
Re: Standard binding free energy protein-ligand (ABF) Giacomo Fiorin (Thu Aug 15 2019 - 08:14:09 CDT)
Re: Standard binding free energy protein-ligand (ABF) philippe Bourly (Thu Aug 15 2019 - 07:04:44 CDT)
Re: Standard binding free energy protein-ligand (ABF) Haohao Fu (Thu Aug 15 2019 - 06:22:07 CDT)
Standard binding free energy protein-ligand (ABF) philippe Bourly (Thu Aug 15 2019 - 06:10:48 CDT)
Standard binding free energy protein-ligand (ABF) philippe Bourly (Thu Aug 15 2019 - 06:03:33 CDT)
Compiler and version used by jenkins to test patch sets Marcelo C. R. Melo (Tue Aug 13 2019 - 08:49:53 CDT)
REST and Periodic Cell Issues Stix, Robyn (NIH/NHLBI) [F] (Mon Aug 12 2019 - 08:34:51 CDT)
ABF and Kinetic Barriers McGuire, Kelly (Sun Aug 11 2019 - 19:26:00 CDT)
Re: AMBER force field parameters Victor Kwan (Thu Aug 08 2019 - 06:51:07 CDT)
constraint-force constant Rui Chen (Tue Aug 06 2019 - 21:28:06 CDT)
Re: Computational electrophysiology Gumbart, JC (Tue Aug 06 2019 - 20:21:49 CDT)
AMBER force field parameters Rui Chen (Tue Aug 06 2019 - 16:22:06 CDT)
Re: Computational electrophysiology Giacomo Fiorin (Mon Aug 05 2019 - 07:56:25 CDT)
Computational electrophysiology Villalain Boullon, Jose (Mon Aug 05 2019 - 06:09:47 CDT)
Same timestep for my simulation run is coming more than once and in random order in the log file Chandni Tiwari (Sun Aug 04 2019 - 09:25:36 CDT)
Re: Re: FATAL ERROR: Must have either an initial temperature or a velocity file è¾›å¿—å® (Sun Aug 04 2019 - 07:22:13 CDT)
RE: mpirun was unable to find the specified executable file Vermaas, Joshua (Fri Aug 02 2019 - 12:16:11 CDT)
Re: mpirun was unable to find the specified executable file Adupa Vasista (Fri Aug 02 2019 - 11:29:28 CDT)
Re: mpirun was unable to find the specified executable file Roshan Shrestha (Fri Aug 02 2019 - 10:13:24 CDT)
Re: mpirun was unable to find the specified executable file mariano spivak (Fri Aug 02 2019 - 10:01:38 CDT)
mpirun was unable to find the specified executable file Adupa Vasista (Fri Aug 02 2019 - 08:24:05 CDT)
Re: FATAL ERROR: Must have either an initial temperature or a velocity file Joao Ribeiro (Thu Aug 01 2019 - 08:55:49 CDT)
Re: Re: FATAL ERROR: Must have either an initial temperature or a velocity file è¾›å¿—å® (Tue Jul 30 2019 - 20:50:47 CDT)
Re: FATAL ERROR: Must have either an initial temperature or a velocity file Joao Ribeiro (Tue Jul 30 2019 - 10:27:55 CDT)
Re: FATAL ERROR: Must have either an initial temperature or a velocity file Joao Ribeiro (Tue Jul 30 2019 - 09:16:13 CDT)
Orientation Colvars Question Xander Gonzalez (Mon Jul 29 2019 - 17:17:27 CDT)
Re: FATAL ERROR: Must have either an initial temperature or a velocity file Joao Ribeiro (Mon Jul 29 2019 - 09:03:36 CDT)
RE: FATAL ERROR: Must have either an initial temperature or a velocity file Vermaas, Joshua (Sun Jul 28 2019 - 14:40:58 CDT)
FATAL ERROR: Must have either an initial temperature or a velocity file è¾›å¿—å® (Sat Jul 27 2019 - 22:48:17 CDT)
Multi-node job errors Anup Prasad (Sat Jul 27 2019 - 02:34:00 CDT)
Some questions about restrained-ensemble molecular dynamics (reMD) TeYu Kao (Wed Jul 24 2019 - 21:13:03 CDT)
Re: namdstats.tcl problem Jeff Comer (Wed Jul 24 2019 - 20:56:53 CDT)
namdstats.tcl problem Rui Chen (Wed Jul 24 2019 - 17:24:46 CDT)
Re: Acceptable Timescale fro NAMD Oscar Bastidas (Wed Jul 24 2019 - 14:32:03 CDT)
Re: Acceptable Timescale fro NAMD Axel Kohlmeyer (Wed Jul 24 2019 - 14:22:32 CDT)
Re: Acceptable Timescale fro NAMD Oscar Bastidas (Wed Jul 24 2019 - 13:49:34 CDT)
question Mandana Tarakamesamani (Wed Jul 24 2019 - 13:39:20 CDT)
Re: Calculating Interaction Energies Using NAMD Energy Plugin Peter Freddolino (Wed Jul 24 2019 - 13:23:51 CDT)
Re: Acceptable Timescale fro NAMD Bassam Haddad (Wed Jul 24 2019 - 13:20:48 CDT)
Acceptable Timescale fro NAMD Oscar Bastidas (Wed Jul 24 2019 - 12:33:38 CDT)
Calculating Interaction Energies Using NAMD Energy Plugin Joanna Zienkiewicz (Wed Jul 24 2019 - 11:41:58 CDT)
Re: Simulation crashes during annealing the reverted all-atom structure Peter Freddolino (Wed Jul 24 2019 - 00:17:22 CDT)
Hydrogen mass repartitioning and 4-fs time steps in NAMD Gumbart, JC (Fri Jul 19 2019 - 11:34:28 CDT)
Re: Issue With CatDCD in Dynamical Network Tutorial Victor Kwan (Mon Jul 15 2019 - 09:45:04 CDT)
Re: Simulation crashes during annealing the reverted all-atom structure Peter Freddolino (Sat Jul 13 2019 - 22:09:46 CDT)
Simulation crashes during annealing the reverted all-atom structure Rabeta Yeasmin (Fri Jul 12 2019 - 16:11:25 CDT)
GLA (Î³-carboxyglutamic acid) topology for CHARMM36 Raul Araya (Fri Jul 12 2019 - 09:00:15 CDT)
Error in running NAMD on a cluster Monika Madhavi (Fri Jul 12 2019 - 08:36:21 CDT)
RE: PMF calculation Mahdi Mousaei (Thu Jul 11 2019 - 15:59:42 CDT)
Re: PMF calculation Giacomo Fiorin (Thu Jul 11 2019 - 15:28:20 CDT)
RE: PMF calculation Mahdi Mousaei (Thu Jul 11 2019 - 15:11:32 CDT)
Re: PMF calculation Souvik Sinha (Thu Jul 11 2019 - 15:08:08 CDT)
PMF calculation Mahdi Mousaei (Thu Jul 11 2019 - 14:14:37 CDT)
Does umbrella sampling need same sampling steps for each windows? jiali wang (Thu Jul 11 2019 - 12:59:32 CDT)
String Method with Swarms of Trajectories (SMwST) Performance Alexander Adams (Thu Jul 11 2019 - 10:43:25 CDT)
New version of Molefacture -small molecule modeling tool- posted Joao Ribeiro (Wed Jul 10 2019 - 16:59:50 CDT)
Issue With CatDCD in Dynamical Network Tutorial Nisler, Collin R. (Wed Jul 10 2019 - 15:50:14 CDT)
Re: Colvars Orientation Question Giacomo Fiorin (Wed Jul 10 2019 - 13:28:16 CDT)
Fwd: Colvars Orientation Question Xander Gonzalez (Wed Jul 10 2019 - 13:18:33 CDT)
Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG2O4 CG311 (ATOMS 1220 1222) Aravinda Munasinghe (Wed Jul 10 2019 - 06:57:20 CDT)
Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG2O4 CG311 (ATOMS 1220 1222) Nirmitee Mulgaonkar (Wed Jul 10 2019 - 01:02:53 CDT)
Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG2O4 CG311 (ATOMS 1220 1222) Aravinda Munasinghe (Tue Jul 09 2019 - 22:00:31 CDT)
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CG2O4 CG311 (ATOMS 1220 1222) Nirmitee Mulgaonkar (Tue Jul 09 2019 - 20:23:49 CDT)
Reminder NAMD Developer Meeting 2019 giuseppe_at_ks.uiuc.edu (Tue Jul 09 2019 - 10:54:29 CDT)
Re: EPW "ATOMS Moving too fast" Bowman, Jacob (Tue Jul 09 2019 - 09:52:34 CDT)
Re: EPW "ATOMS Moving too fast" Peter Freddolino (Tue Jul 09 2019 - 09:24:44 CDT)
Re: EPW "ATOMS Moving too fast" Natalia Ostrowska (Tue Jul 09 2019 - 03:29:26 CDT)
Re: AutoPSF charge generation Srijita Paul (Tue Jul 09 2019 - 00:18:29 CDT)
Re: Velocity unit soroush ziaei (Mon Jul 08 2019 - 15:55:30 CDT)
EPW "ATOMS Moving too fast" Bowman, Jacob (Mon Jul 08 2019 - 15:26:40 CDT)
Re: AutoPSF charge generation Peter Freddolino (Sat Jul 06 2019 - 21:00:48 CDT)
AutoPSF charge generation Adupa Vasista (Sat Jul 06 2019 - 04:28:55 CDT)
Re: Colvars Orientation Question Xander Gonzalez (Fri Jul 05 2019 - 14:22:34 CDT)
Re: Re: vmd-l: Getting the topology,PSF files Adupa Vasista (Fri Jul 05 2019 - 00:04:32 CDT)
Re: Re: vmd-l: Getting the topology,PSF files Pratik Narain Srivastava (Thu Jul 04 2019 - 23:54:54 CDT)
Re: Re: vmd-l: Getting the topology,PSF files Adupa Vasista (Thu Jul 04 2019 - 23:22:37 CDT)
Re: vmd-l: Getting the topology,PSF files Peter Freddolino (Thu Jul 04 2019 - 17:09:41 CDT)
Getting the topology,PSF files Adupa Vasista (Thu Jul 04 2019 - 14:54:25 CDT)
Re: Colvars Orientation Question Xander Gonzalez (Tue Jul 02 2019 - 16:46:11 CDT)
Re: Colvars Orientation Question Giacomo Fiorin (Mon Jul 01 2019 - 19:01:39 CDT)
Re: readmol2 warning: non-unique atoms were renamed. Adupa Vasista (Mon Jul 01 2019 - 15:12:29 CDT)
Colvars Orientation Question Alexander Gonzalez (Mon Jul 01 2019 - 14:59:26 CDT)
Re: readmol2 warning: non-unique atoms were renamed. Joao Ribeiro (Mon Jul 01 2019 - 09:12:22 CDT)
readmol2 warning: non-unique atoms were renamed. Adupa Vasista (Sat Jun 29 2019 - 11:30:25 CDT)
Re: does any body know why GPU Acceleration not work on Windows? Bryan Roessler (Fri Jun 28 2019 - 14:52:47 CDT)
Re: Reload molecular topology for amber files? David Hardy (Fri Jun 28 2019 - 12:12:57 CDT)
AW: does any body know why GPU Acceleration not work on Windows? Norman Geist (Fri Jun 28 2019 - 03:06:21 CDT)
Re: does any body know why GPU Acceleration not work on Windows? Milad Lagzian (Fri Jun 28 2019 - 02:36:16 CDT)
AW: does any body know why GPU Acceleration not work on Windows? Norman Geist (Fri Jun 28 2019 - 02:22:53 CDT)
Re: does any body know why GPU Acceleration not work on Windows? Pratik Narain Srivastava (Fri Jun 28 2019 - 02:18:04 CDT)
Re: does any body know why GPU Acceleration not work on Windows? Miro Astore (Fri Jun 28 2019 - 00:21:46 CDT)
does any body know why GPU Acceleration not work on Windows? Milad Lagzian (Fri Jun 28 2019 - 00:13:49 CDT)
Re: Re: When using WHAM TO ANALYSIS Jiali Wang (Thu Jun 27 2019 - 15:10:40 CDT)
Re: When using WHAM TO ANALYSIS Giacomo Fiorin (Thu Jun 27 2019 - 15:01:47 CDT)
Re: Velocity unit Victor Kwan (Thu Jun 27 2019 - 14:09:19 CDT)
Reload molecular topology for amber files? Norman Geist (Thu Jun 27 2019 - 06:52:49 CDT)
AW: Velocity unit Norman Geist (Thu Jun 27 2019 - 06:06:54 CDT)
Velocity unit Ashkan Shekaari (Thu Jun 27 2019 - 05:47:38 CDT)
Re: Standard Error Calcuation Giacomo Fiorin (Wed Jun 26 2019 - 17:20:57 CDT)
Standard Error Calcuation Mahdi Mousaei (Wed Jun 26 2019 - 17:01:15 CDT)
Re: Question about PMF calculation Giacomo Fiorin (Tue Jun 25 2019 - 11:14:19 CDT)
Re: CUDA acceleration on Windows 10 doesn't work Sunny (Tue Jun 25 2019 - 02:06:25 CDT)
Re: OPC Water Model Brian Radak (Mon Jun 24 2019 - 09:06:32 CDT)
Re: OPC Water Model Peter Freddolino (Mon Jun 24 2019 - 07:18:10 CDT)
Re: CUDA acceleration on Windows 10 doesn't work Milad Lagzian (Mon Jun 24 2019 - 07:09:44 CDT)
OPC Water Model eee ffff (Mon Jun 24 2019 - 05:09:12 CDT)
Re: CUDA acceleration on Windows 10 doesn't work Sunny (Sat Jun 22 2019 - 21:42:58 CDT)
Re: Bug in NAMD Pawel Kedzierski (Sat Jun 22 2019 - 04:52:43 CDT)
Re: Bug in NAMD Marcelo C. R. Melo (Fri Jun 21 2019 - 11:27:15 CDT)
Re: Bug in NAMD Pawel Kedzierski (Fri Jun 21 2019 - 07:01:03 CDT)
Re: Bug in NAMD (was: Big oscillations during QM/MM minimization) Pawel Kedzierski (Thu Jun 20 2019 - 10:35:11 CDT)
Re: Bug in NAMD (was: Big oscillations during QM/MM minimization) Pawel Kedzierski (Thu Jun 20 2019 - 10:11:19 CDT)
Re: Bug in NAMD Marcelo C. R. Melo (Thu Jun 20 2019 - 09:46:36 CDT)
Re: Bug in NAMD Pawel Kedzierski (Thu Jun 20 2019 - 08:23:43 CDT)
CUDA acceleration on Windows 10 doesn't work Maximilian Ebert (Thu Jun 20 2019 - 02:43:05 CDT)
NAMD on Windows 10 with huge performance drop after 39 CPUs Maximilian Ebert (Thu Jun 20 2019 - 02:41:41 CDT)
Immediate postdoc opening in Bio-molecular simulation, University of Alberta, Canada Marawan Hussien (Wed Jun 19 2019 - 19:17:55 CDT)
NAMD Developer Meeting 2019 giuseppe_at_ks.uiuc.edu (Wed Jun 19 2019 - 17:13:31 CDT)
Attachments allowed? Maximilian Ebert (Wed Jun 19 2019 - 11:20:13 CDT)
Re: compiling infiniband version of NAMD Aravinda Munasinghe (Wed Jun 19 2019 - 10:17:07 CDT)
compiling infiniband version of NAMD Kosar Khajeh (Wed Jun 19 2019 - 07:41:27 CDT)
Re: Bug in NAMD (was: Big oscillations during QM/MM minimization) Brian Radak (Tue Jun 18 2019 - 11:42:02 CDT)
Re: Big oscillations during QM/MM minimization mariano spivak (Tue Jun 18 2019 - 09:57:34 CDT)
Bug in NAMD (was: Big oscillations during QM/MM minimization) Pawel Kedzierski (Tue Jun 18 2019 - 01:47:24 CDT)
Re: colvar setting, targetcenters not working jiali wang (Mon Jun 17 2019 - 09:20:41 CDT)
colvar setting, targetcenters not working Jiali Wang (Sun Jun 16 2019 - 20:16:49 CDT)
FATAL ERROR: High global CUDA exclusion count! Sunny (Wed Jun 12 2019 - 12:07:23 CDT)
Re: TMD Partial Fitting Problem mert gÃ¶lcÃ¼k (Wed Jun 12 2019 - 09:32:07 CDT)
FATAL ERROR: High global CUDA exclusion count! Nima Nouri (Wed Jun 12 2019 - 03:20:20 CDT)
Re: TMD Partial Fitting Problem Gumbart, JC (Tue Jun 11 2019 - 18:53:35 CDT)
RE: error in compiling namd Vermaas, Joshua (Tue Jun 11 2019 - 08:00:46 CDT)
error in compiling namd Kosar Khajeh (Tue Jun 11 2019 - 07:45:38 CDT)
TMD Partial Fitting Problem mert gÃ¶lcÃ¼k (Tue Jun 11 2019 - 07:26:02 CDT)
Re: we apply a harmonic potential Giacomo Fiorin (Mon Jun 10 2019 - 12:38:36 CDT)
Re: we apply a harmonic potential Giacomo Fiorin (Sun Jun 09 2019 - 15:18:55 CDT)
Re: Prevent DNA denaturation Takeru KAMEDA (Fri Jun 07 2019 - 08:27:26 CDT)
Re: Problem in Running CUDA-Enabled NAMD Via MOE software Victor Kwan (Fri Jun 07 2019 - 08:21:02 CDT)
Problem in Running CUDA-Enabled NAMD Via MOE software Milad Lagzian (Fri Jun 07 2019 - 04:26:04 CDT)
Re: reg: quenching NAMD trajectory Brian Radak (Thu Jun 06 2019 - 16:37:56 CDT)
Re: reg: quenching NAMD trajectory Lara rajam (Thu Jun 06 2019 - 14:47:22 CDT)
Re: reg: quenching NAMD trajectory Pratik Narain Srivastava (Thu Jun 06 2019 - 14:44:39 CDT)
reg: quenching NAMD trajectory Lara rajam (Thu Jun 06 2019 - 14:39:52 CDT)
Re: Prevent DNA denaturation Ryan McGreevy (Thu Jun 06 2019 - 10:36:45 CDT)
Re: Prevent DNA denaturation Brian Radak (Thu Jun 06 2019 - 10:27:29 CDT)
Re: vecsub:two vectors don't have the same size Joao Ribeiro (Thu Jun 06 2019 - 09:21:58 CDT)
Re: Prevent DNA denaturation Priyanka Mondal (Thu Jun 06 2019 - 08:17:29 CDT)
Prevent DNA denaturation Takeru KAMEDA (Thu Jun 06 2019 - 03:40:48 CDT)
vecsub:two vectors don't have the same size SHRUTEE JEURKAR (Thu Jun 06 2019 - 02:29:47 CDT)
Re: multiplot: Data vector empty, ignoring plot! Adupa Vasista (Wed Jun 05 2019 - 09:20:17 CDT)
Re: multiplot: Data vector empty, ignoring plot! Joao Ribeiro (Wed Jun 05 2019 - 08:51:25 CDT)
Re: multiplot: Data vector empty, ignoring plot! Pratik Narain Srivastava (Wed Jun 05 2019 - 08:41:45 CDT)
Re: multiplot: Data vector empty, ignoring plot! Adupa Vasista (Wed Jun 05 2019 - 08:36:39 CDT)
Re: multiplot: Data vector empty, ignoring plot! Roshan Shrestha (Wed Jun 05 2019 - 08:29:35 CDT)
Re: multiplot: Data vector empty, ignoring plot! Adupa Vasista (Wed Jun 05 2019 - 08:26:20 CDT)
Re: multiplot: Data vector empty, ignoring plot! Pratik Narain Srivastava (Wed Jun 05 2019 - 08:26:30 CDT)
multiplot: Data vector empty, ignoring plot! Adupa Vasista (Wed Jun 05 2019 - 08:18:01 CDT)
Re: NAMD with infinite cutoffs? Brian Radak (Tue Jun 04 2019 - 08:49:36 CDT)
AW: NAMD with infinite cutoffs? Norman Geist (Tue Jun 04 2019 - 08:40:09 CDT)
Re: NAMD with infinite cutoffs? Brian Radak (Tue Jun 04 2019 - 07:59:19 CDT)
Re: Reg: Solvation box Adupa Vasista (Tue Jun 04 2019 - 01:37:20 CDT)
RE: NAMD with infinite cutoffs? Geist, Norman (Mon Jun 03 2019 - 23:58:49 CDT)
RE: NAMD with infinite cutoffs? Vermaas, Joshua (Mon Jun 03 2019 - 17:01:53 CDT)
Re: NAMD with infinite cutoffs? Geist, Norman (Mon Jun 03 2019 - 15:45:40 CDT)
Re: NAMD with infinite cutoffs? Brian Radak (Mon Jun 03 2019 - 13:21:15 CDT)
NAMD with infinite cutoffs? Geist, Norman (Mon Jun 03 2019 - 11:30:24 CDT)
Re: Reg: Solvation box Adupa Vasista (Sun Jun 02 2019 - 08:48:29 CDT)
Re: Reg: Solvation box Jim Parker (Sun Jun 02 2019 - 08:28:21 CDT)
Re: Reg: Solvation box Adupa Vasista (Sun Jun 02 2019 - 08:18:33 CDT)
Re: Reg: Solvation box Pratik Narain Srivastava (Sun Jun 02 2019 - 08:13:06 CDT)
Re: Reg: Solvation box Adupa Vasista (Sun Jun 02 2019 - 08:03:28 CDT)
Re: Reg: Solvation box Axel Kohlmeyer (Sun Jun 02 2019 - 06:42:45 CDT)
Reg: Solvation box Adupa Vasista (Sun Jun 02 2019 - 03:50:50 CDT)
Re: Reg: Docking Pratik Narain Srivastava (Sat Jun 01 2019 - 07:06:54 CDT)
Reg: Docking Adupa Vasista (Sat Jun 01 2019 - 05:08:11 CDT)
Re: Reg: Force Field file Adupa Vasista (Fri May 31 2019 - 01:57:09 CDT)
Re: Reg: Force Field file Roshan Shrestha (Fri May 31 2019 - 01:59:25 CDT)
Re: Reg: Force Field file Adupa Vasista (Fri May 31 2019 - 01:50:57 CDT)
Re: Reg: Force Field file Pratik Narain Srivastava (Fri May 31 2019 - 01:53:13 CDT)
Reg: Force Field file Adupa Vasista (Fri May 31 2019 - 01:47:28 CDT)
Distortion in Structure Minimization HEMANTH H 18310019 (Mon May 27 2019 - 02:01:58 CDT)
Re: FATAL ERROR: Periodic cell has become too small for original patch grid! HEMANTH H 18310019 (Sun May 26 2019 - 21:38:33 CDT)
Re: FATAL ERROR: Periodic cell has become too small for original patch grid! Aravinda Munasinghe (Sun May 26 2019 - 13:29:41 CDT)
FATAL ERROR: Periodic cell has become too small for original patch grid! Adupa Vasista (Sun May 26 2019 - 07:07:39 CDT)
Re: how to switch off hydrogen bonds in TIP4P/2005 water Jeff Comer (Sat May 25 2019 - 15:11:19 CDT)
Re: how to switch off hydrogen bonds in TIP4P/2005 water Axel Kohlmeyer (Sat May 25 2019 - 12:50:45 CDT)
Re: Ingrid Bernardes Santana Martins (Sat May 25 2019 - 06:49:03 CDT)
Re: Axel Kohlmeyer (Sat May 25 2019 - 06:24:15 CDT)
Re: Axel Kohlmeyer (Sat May 25 2019 - 06:17:28 CDT)
Re: Ingrid Bernardes Santana Martins (Sat May 25 2019 - 06:05:29 CDT)
(no subject) Adupa Vasista (Sat May 25 2019 - 05:45:51 CDT)
how to switch off hydrogen bonds in TIP4P/2005 water Monika Madhavi (Fri May 24 2019 - 08:43:59 CDT)
"constraint failure in rattle algorithm" soroush ziaei (Tue May 21 2019 - 17:31:21 CDT)
Running broken-symmetry with namd-orca Francesco Pietra (Tue May 21 2019 - 10:59:29 CDT)
Re: PME with Implicit solvent - Reg Jeff Comer (Mon May 20 2019 - 17:03:04 CDT)
Re: PME with Implicit solvent - Reg Brian Radak (Mon May 20 2019 - 13:55:21 CDT)
Re: compiling NAMD 2.13 make error Priyanka Mondal (Mon May 20 2019 - 13:22:17 CDT)
Re: PME with Implicit solvent - Reg Mani Kandan (Mon May 20 2019 - 12:58:53 CDT)
Re: PME with Implicit solvent - Reg Brian Radak (Mon May 20 2019 - 12:51:40 CDT)
PME with Implicit solvent - Reg Mani Kandan (Mon May 20 2019 - 08:58:32 CDT)
Re: vacuum simulation -Reg Mani Kandan (Sun May 19 2019 - 11:23:23 CDT)
Re: vacuum simulation -Reg Subbarao Kanchi (Sun May 19 2019 - 10:32:33 CDT)
Re: vacuum simulation -Reg Mani Kandan (Sun May 19 2019 - 10:27:47 CDT)
Re: vacuum simulation -Reg Subbarao Kanchi (Sun May 19 2019 - 09:33:18 CDT)
Re: vacuum simulation -Reg Mani Kandan (Sun May 19 2019 - 09:27:36 CDT)
Re: vacuum simulation -Reg Ashkan Shekaari (Sun May 19 2019 - 09:08:11 CDT)
vacuum simulation -Reg Mani Kandan (Sun May 19 2019 - 08:55:02 CDT)
catalysis mechnism of ATPase sunyeping (Sun May 19 2019 - 06:30:07 CDT)
Re: compiling NAMD 2.13 make error Giacomo Fiorin (Sat May 18 2019 - 14:46:52 CDT)
compiling NAMD 2.13 make error Kosar Khajeh (Sat May 18 2019 - 04:37:44 CDT)
Compiler segfault when building 2.13 with GCC 8.x fabricio (Wed May 15 2019 - 13:51:28 CDT)
Re: Make error in compiling NAMD source code Priyanka Mondal (Wed May 15 2019 - 09:52:16 CDT)
Make error in compiling NAMD source code Kosar Khajeh (Wed May 15 2019 - 04:21:50 CDT)
MD without water - Reg Mani Kandan (Mon May 13 2019 - 13:11:31 CDT)
Re: " the error of hydrogen group size " soroush ziaei (Fri May 10 2019 - 09:22:06 CDT)
RE: " the error of hydrogen group size " Lennart Nilsson (Fri May 10 2019 - 08:47:12 CDT)
Re: " the error of hydrogen group size " soroush ziaei (Fri May 10 2019 - 08:28:44 CDT)
AW: patch for cystein bond Bernitzky, Cornelius Constantin Maria (Thu May 09 2019 - 03:48:07 CDT)
RE: patch for cystein bond Lennart Nilsson (Wed May 08 2019 - 15:10:34 CDT)
RE: patch for cystein bond Vermaas, Joshua (Wed May 08 2019 - 13:37:31 CDT)
Re: patch for cystein bond Brian Radak (Wed May 08 2019 - 13:15:27 CDT)
patch for cystein bond Bernitzky, Cornelius Constantin Maria (Wed May 08 2019 - 09:28:01 CDT)
Re: Need help with psfgen : psfgen can't read file.pdb Joao Ribeiro (Tue May 07 2019 - 10:53:30 CDT)
Re: Need help with psfgen : psfgen can't read file.pdb Brian Radak (Tue May 07 2019 - 10:44:39 CDT)
Re: Big oscillations during QM/MM minimization Dawid das (Tue May 07 2019 - 10:07:20 CDT)
Re: Need help with psfgen : psfgen can't read file.pdb Priyanka Mondal (Tue May 07 2019 - 10:05:37 CDT)
Big oscillations during QM/MM minimization Pawel Kedzierski (Tue May 07 2019 - 08:53:18 CDT)
Re: Need help with psfgen : psfgen can't read file.pdb Brian Radak (Tue May 07 2019 - 08:16:01 CDT)
Re: Need help with psfgen : psfgen can't read file.pdb Victor Kwan (Tue May 07 2019 - 01:46:43 CDT)
Need help with psfgen : psfgen can't read file.pdb Priyanka Mondal (Mon May 06 2019 - 20:53:03 CDT)
Re: " the error of hydrogen group size " Brian Radak (Fri May 03 2019 - 12:37:25 CDT)
Re: " the error of hydrogen group size " soroush ziaei (Fri May 03 2019 - 09:48:06 CDT)
Re: orca_plot asking .xyz file from QM-MM Francesco Pietra (Fri May 03 2019 - 08:18:43 CDT)
Re: " the error of hydrogen group size " soroush ziaei (Fri May 03 2019 - 05:56:55 CDT)
Re: Question McGuire, Kelly (Thu May 02 2019 - 14:04:31 CDT)
Re: Question Brian Radak (Thu May 02 2019 - 13:59:15 CDT)
orca_plot asking .xyz file from QM-MM Francesco Pietra (Thu May 02 2019 - 13:03:16 CDT)
Question McGuire, Kelly (Thu May 02 2019 - 12:10:41 CDT)
Re: How to extend an ABF simulation ? Giacomo Fiorin (Wed May 01 2019 - 09:43:54 CDT)
Re: " the error of hydrogen group size " Brian Radak (Wed May 01 2019 - 08:51:08 CDT)
Re: How to extend an ABF simulation ? philippe Bourly (Wed May 01 2019 - 02:55:29 CDT)
How do I add passivated H-atom to ZGNR Priyanka Mondal (Tue Apr 30 2019 - 11:43:20 CDT)
Re: How to extend an ABF simulation ? horacio poblete (Tue Apr 30 2019 - 10:36:49 CDT)
How to extend an ABF simulation ? philippe Bourly (Tue Apr 30 2019 - 10:19:38 CDT)
MD Simulations with GROMACS/NAMD/AMBER/VMD: Seasonal School in Stockholm 10-13 June Joao Ribeiro (Tue Apr 30 2019 - 09:43:46 CDT)
" the error of hydrogen group size " soroush ziaei (Tue Apr 30 2019 - 04:25:57 CDT)
FW (1): 71i sudipta.mml (Mon Apr 29 2019 - 04:45:45 CDT)
Error in the NAMD Tutorial Ashkan Shekaari (Sat Apr 27 2019 - 08:39:21 CDT)
Re: Number of QM Atoms Error McGuire, Kelly (Fri Apr 26 2019 - 18:18:04 CDT)
Postdoc Position at Penn in Chromosome Modeling Hemant Kumar (Fri Apr 26 2019 - 13:41:25 CDT)
Re: vmd-l: Bugs and Questions McGuire, Kelly (Thu Apr 25 2019 - 14:25:02 CDT)
Re: vmd-l: Bugs and Questions Joao Ribeiro (Thu Apr 25 2019 - 14:22:44 CDT)
Re: vmd-l: Bugs and Questions McGuire, Kelly (Thu Apr 25 2019 - 14:15:36 CDT)
Re: vmd-l: Bugs and Questions Joao Ribeiro (Thu Apr 25 2019 - 14:14:17 CDT)
Re: vmd-l: Bugs and Questions McGuire, Kelly (Thu Apr 25 2019 - 14:10:36 CDT)
Re: vmd-l: Bugs and Questions Joao Ribeiro (Thu Apr 25 2019 - 13:39:32 CDT)
Bugs and Questions McGuire, Kelly (Thu Apr 25 2019 - 10:14:02 CDT)
Number of QM Atoms Error McGuire, Kelly (Wed Apr 24 2019 - 18:19:45 CDT)
Re: Water Molecule Issue McGuire, Kelly (Wed Apr 24 2019 - 12:54:01 CDT)
Re: Water Molecule Issue McGuire, Kelly (Wed Apr 24 2019 - 10:12:29 CDT)
Water Molecule Issue McGuire, Kelly (Wed Apr 24 2019 - 10:03:23 CDT)
RE: Umbrella Sampling in PLUMED + NAMD Vermaas, Joshua (Tue Apr 23 2019 - 09:53:12 CDT)
Adding H-bonds to neutralize GNR built using Nanotube Builder in VMD Priyanka Mondal (Tue Apr 23 2019 - 09:30:26 CDT)
Re: Error in PMF Calculations HEMANTH H 18310019 (Tue Apr 23 2019 - 07:06:06 CDT)
RE: Umbrella Sampling in PLUMED + NAMD Vermaas, Joshua (Mon Apr 22 2019 - 11:50:56 CDT)
Umbrella Sampling in PLUMED + NAMD Mikhail Suyetin (Mon Apr 22 2019 - 01:33:04 CDT)
Enthalpy Question McGuire, Kelly (Mon Apr 22 2019 - 00:19:09 CDT)
Re: Parameter and Topology File Question Brian Radak (Sun Apr 21 2019 - 12:30:49 CDT)
Re: Parameter and Topology File Question Victor Kwan (Sun Apr 21 2019 - 07:35:53 CDT)
Parameter and Topology File Question Oscar Bastidas (Sun Apr 21 2019 - 04:44:45 CDT)
Re: Problem with namd 2.13 constant pH molecular dynamics, HSD residue. Brian Radak (Fri Apr 19 2019 - 08:33:04 CDT)
Problem with namd 2.13 constant pH molecular dynamics, HSD residue. Ingrid Bernardes Santana Martins (Fri Apr 19 2019 - 08:01:32 CDT)
Re: About changing charge/multiplicity during QM-MM Gerard Rowe (Fri Apr 19 2019 - 07:46:31 CDT)
Re: Tutorial McGuire, Kelly (Thu Apr 18 2019 - 18:06:25 CDT)
Re: Tutorial Marcelo C. R. Melo (Thu Apr 18 2019 - 14:33:24 CDT)
Tutorial McGuire, Kelly (Thu Apr 18 2019 - 12:42:17 CDT)
Re: Re: Error while equilibrating AGNR nanopore + DNA system Victor Kwan (Tue Apr 16 2019 - 06:02:50 CDT)
Re: Error while equilibrating AGNR nanopore + DNA system Priyanka Mondal (Mon Apr 15 2019 - 12:27:31 CDT)
Re: Building of NAMD on the Linux cluster with InfiniBand Aravinda Munasinghe (Mon Apr 15 2019 - 10:41:08 CDT)
Re: changing value of coulomb constant Brian Radak (Mon Apr 15 2019 - 09:51:36 CDT)
Error while equilibrating AGNR nanopore + DNA system Priyanka Mondal (Mon Apr 15 2019 - 09:45:52 CDT)
Re: changing value of coulomb constant Gumbart, JC (Mon Apr 15 2019 - 09:05:29 CDT)
Re: About changing charge/multiplicity during QM-MM Gerard Rowe (Mon Apr 15 2019 - 08:06:52 CDT)
Building of NAMD on the Linux cluster with InfiniBand ÐÑ€ÑÐ»Ð°Ð½ ÐšÑƒÑÐ¼Ð°ÐµÐ² (Mon Apr 15 2019 - 06:06:12 CDT)
Re: changing value of coulomb constant Brian Radak (Sun Apr 14 2019 - 11:47:16 CDT)
changing value of coulomb constant Akshay Prabhakant (Sun Apr 14 2019 - 01:26:40 CDT)
Re: Non bonding energy calculation through NAMD Pratik Narain Srivastava (Fri Apr 12 2019 - 14:03:43 CDT)
Re: Non bonding energy calculation through NAMD Peter Freddolino (Fri Apr 12 2019 - 14:02:34 CDT)
Re: Non bonding energy calculation through NAMD Gumbart, JC (Fri Apr 12 2019 - 13:04:16 CDT)
Re: Electrostatic interaction of 2 ions Fateme Ghadirian (Fri Apr 12 2019 - 12:39:54 CDT)
Re: Electrostatic interaction of 2 ions Brian Radak (Fri Apr 12 2019 - 10:07:36 CDT)
Electrostatic interaction of 2 ions Fateme Ghadirian (Fri Apr 12 2019 - 09:33:08 CDT)
Re: Umbrella sampling of a protein through a membrane Giacomo Fiorin (Fri Apr 12 2019 - 09:12:38 CDT)
Re: Non bonding energy calculation through NAMD Brian Radak (Fri Apr 12 2019 - 08:58:45 CDT)
Re: Non bonding energy calculation through NAMD varun dewaker (Fri Apr 12 2019 - 08:24:39 CDT)
Re: Non bonding energy calculation through NAMD Brian Radak (Fri Apr 12 2019 - 07:49:32 CDT)
Re: Non bonding energy calculation through NAMD varun dewaker (Fri Apr 12 2019 - 02:29:06 CDT)
RE: Umbrella sampling of a protein through a membrane Villalain Boullon, Jose (Fri Apr 12 2019 - 01:49:24 CDT)
RE: Umbrella sampling of a protein through a membrane Villalain Boullon, Jose (Fri Apr 12 2019 - 01:40:34 CDT)
Re: Umbrella sampling of a protein through a membrane Victor Kwan (Thu Apr 11 2019 - 23:04:59 CDT)
Re: Umbrella sampling of a protein through a membrane Gumbart, JC (Thu Apr 11 2019 - 22:59:10 CDT)
Re: Non bonding energy calculation through NAMD Brian Radak (Thu Apr 11 2019 - 08:56:48 CDT)
Umbrella sampling of a protein through a membrane Villalain Boullon, Jose (Thu Apr 11 2019 - 02:00:51 CDT)
Re: Non bonding energy calculation through NAMD varun dewaker (Thu Apr 11 2019 - 01:46:37 CDT)
Python Wrapper Bug McGuire, Kelly (Thu Apr 11 2019 - 01:08:33 CDT)
QM/MM internal energies Shahar Keinan (Wed Apr 10 2019 - 15:18:19 CDT)
Re: Error in PMF Calculations Souvik Sinha (Wed Apr 10 2019 - 03:38:22 CDT)
Re: Error in PMF Calculations Souvik Sinha (Wed Apr 10 2019 - 03:20:21 CDT)
Re: Error in PMF Calculations HEMANTH H 18310019 (Wed Apr 10 2019 - 01:59:53 CDT)
Re: Error in PMF Calculations Souvik Sinha (Wed Apr 10 2019 - 02:02:20 CDT)
Re: Error in PMF Calculations HEMANTH H 18310019 (Tue Apr 09 2019 - 23:42:20 CDT)
FATAL ERROR: CUDA error CudaComputeNonbonded::forceDoneCheck polled 1000000 times over 154.549621 s on Pe 4 (c36.chundoong device 0 pci 0:2:0) ê¹€ë¯¼ìž¬ (Mon Apr 08 2019 - 23:00:38 CDT)
Re: About changing charge/multiplicity during QM-MM Gerard Rowe (Mon Apr 08 2019 - 11:26:48 CDT)
Re: Pointcharge file in QM/MM setup with ORCA Acharya, Atanu (Mon Apr 08 2019 - 09:18:58 CDT)
Re: Merge File Question McGuire, Kelly (Sun Apr 07 2019 - 00:47:23 CDT)
Merge File Question McGuire, Kelly (Fri Apr 05 2019 - 19:36:08 CDT)
Re: Error in PMF Calculations Jeff Comer (Fri Apr 05 2019 - 08:42:08 CDT)
Re: Error in PMF Calculations HEMANTH H 18310019 (Thu Apr 04 2019 - 23:39:21 CDT)
Re: Pointcharge file in QM/MM setup with ORCA Marcelo C. R. Melo (Thu Apr 04 2019 - 15:05:07 CDT)
Re: Error in PMF Calculations Jeff Comer (Thu Apr 04 2019 - 07:16:38 CDT)
Error in PMF Calculations HEMANTH H 18310019 (Thu Apr 04 2019 - 00:21:54 CDT)
TeraChem QMMM McGuire, Kelly (Wed Apr 03 2019 - 17:42:13 CDT)
Re: [NAMD] How to decompose REUS results into electrostatic and van der Waals contributions Jeff Comer (Wed Apr 03 2019 - 15:10:03 CDT)
Pointcharge file in QM/MM setup with ORCA Acharya, Atanu (Wed Apr 03 2019 - 15:05:00 CDT)
Re: [NAMD] How to decompose REUS results into electrostatic and van der Waals contributions Gumbart, JC (Wed Apr 03 2019 - 14:52:38 CDT)
RE: [NAMD] How to decompose REUS results into electrostatic and van der Waals contributions Vermaas, Joshua (Wed Apr 03 2019 - 11:24:50 CDT)
Re: SMD negative forces Joao Ribeiro (Wed Apr 03 2019 - 10:18:06 CDT)
Re: SMD negative forces Joao Ribeiro (Wed Apr 03 2019 - 10:00:17 CDT)
Re: inputPrefix merge error ABF Abhishek TYAGI (Wed Apr 03 2019 - 09:55:00 CDT)
Re: Running MD simulation for two molecules ê¹€ë¯¼ìž¬ (Wed Apr 03 2019 - 01:44:46 CDT)
[NAMD] How to decompose REUS results into electrostatic and van der Waals contributions Canal de Sebassen (Tue Apr 02 2019 - 19:25:08 CDT)
RE: position restraint only certain residues during minimization Vermaas, Joshua (Tue Apr 02 2019 - 12:17:08 CDT)
RE: Running MD simulation for two molecules Vermaas, Joshua (Tue Apr 02 2019 - 12:14:33 CDT)
Re: inputPrefix merge error ABF Giacomo Fiorin (Tue Apr 02 2019 - 12:02:25 CDT)
Re: position restraint only certain residues during minimization Brian Radak (Tue Apr 02 2019 - 11:31:49 CDT)
position restraint only certain residues during minimization Akshay Prabhakant (Tue Apr 02 2019 - 11:14:57 CDT)
Re: About changing charge/multiplicity during QM-MM Gerard Rowe (Tue Apr 02 2019 - 11:14:57 CDT)
Re: inputPrefix merge error ABF Jeff Comer (Tue Apr 02 2019 - 11:03:54 CDT)
Fwd: About changing charge/multiplicity during QM-MM Francesco Pietra (Tue Apr 02 2019 - 09:36:47 CDT)
Re: Non bonding energy calculation through NAMD Giacomo Fiorin (Tue Apr 02 2019 - 09:00:54 CDT)
Non bonding energy calculation through NAMD varun dewaker (Tue Apr 02 2019 - 03:59:15 CDT)
Running MD simulation for two molecules ê¹€ë¯¼ìž¬ (Tue Apr 02 2019 - 01:23:45 CDT)
Re: inputPrefix merge error ABF Abhishek TYAGI (Mon Apr 01 2019 - 22:29:42 CDT)
Re: inputPrefix merge error ABF Jeff Comer (Mon Apr 01 2019 - 15:36:02 CDT)
Re: TeraChem McGuire, Kelly (Mon Apr 01 2019 - 13:54:58 CDT)
Re: TeraChem Gerard Rowe (Mon Apr 01 2019 - 13:39:51 CDT)
Re: TeraChem McGuire, Kelly (Mon Apr 01 2019 - 13:25:39 CDT)
Re: TeraChem Gerard Rowe (Mon Apr 01 2019 - 13:19:39 CDT)
Re: TclBC forces on individual atoms Udaya Dahal (Mon Apr 01 2019 - 11:56:49 CDT)
RE: TclBC forces on individual atoms Vermaas, Joshua (Mon Apr 01 2019 - 11:49:34 CDT)
inputPrefix merge error ABF Abhishek TYAGI (Sun Mar 31 2019 - 23:46:47 CDT)
TclBC forces on individual atoms Udaya Dahal (Sun Mar 31 2019 - 10:24:52 CDT)
Re: MAOL ABOUT USAGE OF TCL SCRIPT Giacomo Fiorin (Sun Mar 31 2019 - 10:01:33 CDT)
MAOL ABOUT USAGE OF TCL SCRIPT Vidhya Sankar (Sun Mar 31 2019 - 03:56:29 CDT)
Re: TeraChem McGuire, Kelly (Sat Mar 30 2019 - 14:21:51 CDT)
Re: TeraChem McGuire, Kelly (Sat Mar 30 2019 - 14:20:18 CDT)
Re: TeraChem Brian Radak (Sat Mar 30 2019 - 14:13:47 CDT)
Re: Restart Annealing McGuire, Kelly (Sat Mar 30 2019 - 13:48:45 CDT)
Restart Annealing McGuire, Kelly (Sat Mar 30 2019 - 12:09:34 CDT)
TeraChem McGuire, Kelly (Fri Mar 29 2019 - 18:29:18 CDT)
QMMM 1 Node vs Multinode McGuire, Kelly (Fri Mar 29 2019 - 14:48:31 CDT)
AW: mpi with NAMD Norman Geist (Fri Mar 29 2019 - 09:42:17 CDT)
Re: mpi with NAMD John Hamre (Fri Mar 29 2019 - 09:38:55 CDT)
AW: mpi with NAMD Norman Geist (Fri Mar 29 2019 - 09:29:10 CDT)
mpi with NAMD John Hamre (Fri Mar 29 2019 - 09:19:09 CDT)
mail about tcl script Vidhya Sankar (Fri Mar 29 2019 - 08:52:34 CDT)
SMD negative forces Seibold, Steve Allan (Fri Mar 29 2019 - 08:37:03 CDT)
Machinefile Question McGuire, Kelly (Thu Mar 28 2019 - 19:34:43 CDT)
Re: About changing charge/multiplicity during QM-MM Francesco Pietra (Thu Mar 28 2019 - 16:19:01 CDT)
Re: About changing charge/multiplicity during QM-MM Francesco Pietra (Thu Mar 28 2019 - 15:04:14 CDT)
Re: About changing charge/multiplicity during QM-MM William Tao (Thu Mar 28 2019 - 12:05:02 CDT)
Re: About changing charge/multiplicity during QM-MM Francesco Pietra (Thu Mar 28 2019 - 11:49:48 CDT)
Re: Fastest way to get PSF file for pure QM simulation? William Tao (Thu Mar 28 2019 - 11:43:29 CDT)
REMD using remote GPU John Hamre (Thu Mar 28 2019 - 08:51:21 CDT)
Re: mail about pbs script John Hamre (Thu Mar 28 2019 - 08:49:41 CDT)
mail about pbs script Vidhya Sankar (Thu Mar 28 2019 - 06:35:47 CDT)
Re: how to translate a protein without unfolding Karteek Bejagam (Wed Mar 27 2019 - 00:46:45 CDT)
how to translate a protein without unfolding Monika Madhavi (Wed Mar 27 2019 - 00:26:29 CDT)
Re: About changing charge/multiplicity during QM-MM Gerard Rowe (Tue Mar 26 2019 - 16:24:05 CDT)
Re: About changing charge/multiplicity during QM-MM Francesco Pietra (Tue Mar 26 2019 - 11:35:23 CDT)
Re: mail about error in configuration files Brian Radak (Mon Mar 25 2019 - 14:53:39 CDT)
Re: About changing charge/multiplicity during QM-MM Gerard Rowe (Mon Mar 25 2019 - 13:34:09 CDT)
Fwd: About changing charge/multiplicity during QM-MM Francesco Pietra (Mon Mar 25 2019 - 13:20:49 CDT)
RE: mail about error in configuration files Vermaas, Joshua (Mon Mar 25 2019 - 12:03:53 CDT)
Re: Re: Solvate with methanol and acetone using free energy methods in NAMD? Brian Radak (Mon Mar 25 2019 - 11:44:08 CDT)
Re: About changing charge/multiplicity during QM-MM Francesco Pietra (Mon Mar 25 2019 - 11:09:41 CDT)
Re: About changing charge/multiplicity during QM-MM Gerard Rowe (Mon Mar 25 2019 - 09:52:18 CDT)
Re: About changing charge/multiplicity during QM-MM Francesco Pietra (Mon Mar 25 2019 - 09:33:55 CDT)
mail about error in configuration files Vidhya Sankar (Mon Mar 25 2019 - 08:59:01 CDT)
Re: About changing charge/multiplicity during QM-MM McGuire, Kelly (Mon Mar 25 2019 - 02:47:14 CDT)
About changing charge/multiplicity during QM-MM Francesco Pietra (Mon Mar 25 2019 - 02:16:35 CDT)
Re: Solvate with methanol and acetone using free energy methods in NAMD? Braden Kelly (Sun Mar 24 2019 - 14:49:40 CDT)
Re: Fastest way to get PSF file for pure QM simulation? William Tao (Sun Mar 24 2019 - 13:33:03 CDT)
Solvate with methanol and acetone using free energy methods in NAMD? Defrese, Matthew (Sun Mar 24 2019 - 13:03:52 CDT)
Re: Fastest way to get PSF file for pure QM simulation? Joao Ribeiro (Sat Mar 23 2019 - 18:47:12 CDT)
Re: Fastest way to get PSF file for pure QM simulation? William Tao (Sat Mar 23 2019 - 14:32:12 CDT)
Re: Fastest way to get PSF file for pure QM simulation? Marcelo C. R. Melo (Sat Mar 23 2019 - 12:25:04 CDT)
Re: Constraint failure in rattle algorithm for some atoms, simulation becomes unstable Brian Radak (Fri Mar 22 2019 - 11:20:26 CDT)
Re: Constraint failure in rattle algorithm for some atoms, simulation becomes unstable Giacomo Fiorin (Fri Mar 22 2019 - 08:08:24 CDT)
Constraint failure in rattle algorithm for some atoms, simulation becomes unstable Akshay Prabhakant (Fri Mar 22 2019 - 05:01:55 CDT)
Fastest way to get PSF file for pure QM simulation? William Tao (Thu Mar 21 2019 - 21:27:42 CDT)
Re: QMMM Frequency Calculation Francesco Pietra (Thu Mar 21 2019 - 17:05:16 CDT)
Re: QMMM Frequency Calculation McGuire, Kelly (Thu Mar 21 2019 - 15:17:44 CDT)
Re: QMMM Frequency Calculation McGuire, Kelly (Thu Mar 21 2019 - 12:25:34 CDT)
RE: QMMM Frequency Calculation Bennion, Brian (Thu Mar 21 2019 - 12:07:18 CDT)
QMMM Frequency Calculation McGuire, Kelly (Thu Mar 21 2019 - 11:55:12 CDT)
Re: what's the latest on using NAMD (and MD in general) for docking? Homeo Morphism (Thu Mar 21 2019 - 02:04:27 CDT)
Re: what's the latest on using NAMD (and MD in general) for docking? Thomas Evangelidis (Wed Mar 20 2019 - 18:42:16 CDT)
Colvar not working in NAMD2.12 Linux version Mukta Sharma (Wed Mar 20 2019 - 18:01:45 CDT)
Average structure using colvars Deepti Karandur (Wed Mar 20 2019 - 15:39:59 CDT)
Re: how to make a .Dx file trajectory to showing the Electrostatic Maps or ion concentration video? Giacomo Fiorin (Wed Mar 20 2019 - 14:42:13 CDT)
what's the latest on using NAMD (and MD in general) for docking? Homeo Morphism (Wed Mar 20 2019 - 13:20:17 CDT)
Re: how to make a .Dx file trajectory to showing the Electrostatic Maps or ion concentration video? Giacomo Fiorin (Wed Mar 20 2019 - 08:10:44 CDT)
how to make a .Dx file trajectory to showing the Electrostatic Maps or ion concentration video? jiali wang (Tue Mar 19 2019 - 20:00:55 CDT)
Re: COMmotion -- is it a good practice to turn it on for a restart? Brian Radak (Tue Mar 19 2019 - 17:03:02 CDT)
COMmotion -- is it a good practice to turn it on for a restart? Homeo Morphism (Tue Mar 19 2019 - 16:30:02 CDT)
Re: Parallel Simulation Question Gerard Rowe (Tue Mar 19 2019 - 14:59:03 CDT)
Re: Parallel Simulation Question McGuire, Kelly (Tue Mar 19 2019 - 14:22:44 CDT)
Re: need help in study the effect of mutation, L- (Tue Mar 19 2019 - 14:14:03 CDT)
Re: Parallel Simulation Question Gerard Rowe (Tue Mar 19 2019 - 13:39:52 CDT)
Re: vmd-l: ORCA Orbital Bug John Stone (Tue Mar 19 2019 - 13:04:58 CDT)
Re: vmd-l: ORCA Orbital Bug McGuire, Kelly (Tue Mar 19 2019 - 12:43:30 CDT)
Re: vmd-l: ORCA Orbital Bug McGuire, Kelly (Tue Mar 19 2019 - 12:40:34 CDT)
Re: vmd-l: ORCA Orbital Bug John Stone (Tue Mar 19 2019 - 12:39:43 CDT)
Re: vmd-l: ORCA Orbital Bug McGuire, Kelly (Tue Mar 19 2019 - 12:31:43 CDT)
Re: Parallel Simulation Question McGuire, Kelly (Mon Mar 18 2019 - 22:57:23 CDT)
RE: Unit of Force constant of position restraint Vermaas, Joshua (Mon Mar 18 2019 - 11:59:53 CDT)
Unit of Force constant of position restraint Junwoong Yoon (Sun Mar 17 2019 - 23:20:07 CDT)
Re: vmd-l: ORCA Orbital Bug McGuire, Kelly (Sun Mar 17 2019 - 19:58:46 CDT)
Re: vmd-l: ORCA Orbital Bug John Stone (Sun Mar 17 2019 - 19:19:48 CDT)
Parallel Simulation Question McGuire, Kelly (Sat Mar 16 2019 - 23:30:08 CDT)
Re: vmd-l: ORCA Orbital Bug McGuire, Kelly (Sat Mar 16 2019 - 18:34:51 CDT)
Re: vmd-l: ORCA Orbital Bug John Stone (Sat Mar 16 2019 - 01:13:06 CDT)
Re: Re: ORCA NAMD Parallel McGuire, Kelly (Fri Mar 15 2019 - 17:22:08 CDT)
Re: Re: ORCA NAMD Parallel Marcelo C. R. Melo (Fri Mar 15 2019 - 16:20:58 CDT)
need help in study the effect of mutation, L- (Fri Mar 15 2019 - 13:01:00 CDT)
ORCA Orbital Bug McGuire, Kelly (Fri Mar 15 2019 - 11:02:30 CDT)
Re: QMMM ORCA Error McGuire, Kelly (Fri Mar 15 2019 - 10:54:43 CDT)
Re: ORCA NAMD Parallel McGuire, Kelly (Fri Mar 15 2019 - 10:53:25 CDT)
Re: QMMM ORCA Error Gerard Rowe (Fri Mar 15 2019 - 09:47:34 CDT)
Re: ORCA NAMD Parallel Gerard Rowe (Fri Mar 15 2019 - 09:45:30 CDT)
alculate energy force field L- (Thu Mar 14 2019 - 11:39:24 CDT)
RE: "the error of movement of atoms" soroush ziaei (Thu Mar 14 2019 - 03:36:25 CDT)
RE: "the error of movement of atoms" soroush ziaei (Thu Mar 14 2019 - 02:59:31 CDT)
ORCA NAMD Parallel McGuire, Kelly (Thu Mar 14 2019 - 02:51:09 CDT)
QMMM ORCA Error McGuire, Kelly (Thu Mar 14 2019 - 01:50:24 CDT)
Re: Re: Didn't Find vdw parameter QMMM McGuire, Kelly (Thu Mar 14 2019 - 01:48:03 CDT)
Re: BUG? reinitatoms on wrapped coordinates occasionally fail with rigidbonds Jim Phillips (Wed Mar 13 2019 - 13:43:16 CDT)
Re: Re: Didn't Find vdw parameter QMMM Jim Phillips (Wed Mar 13 2019 - 13:35:58 CDT)
Re: Re: Didn't Find vdw parameter QMMM Brian Radak (Wed Mar 13 2019 - 10:59:15 CDT)
Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly? yjcoshc_at_gmail.com (Wed Mar 13 2019 - 10:41:47 CDT)
Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly? Giacomo Fiorin (Wed Mar 13 2019 - 10:39:20 CDT)
Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly? yjcoshc_at_gmail.com (Wed Mar 13 2019 - 10:08:55 CDT)
Re: Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly? JÃ©rÃ´me HÃ©nin (Wed Mar 13 2019 - 09:37:31 CDT)
Colvars: Are the derivatives of optimal rotation matrix wrt atomic coordinates applied implicitly? yjcoshc_at_gmail.com (Wed Mar 13 2019 - 08:01:04 CDT)
BUG? reinitatoms on wrapped coordinates occasionally fail with rigidbonds Norman Geist (Wed Mar 13 2019 - 03:05:56 CDT)
Re: Didn't Find vdw parameter QMMM McGuire, Kelly (Tue Mar 12 2019 - 22:13:43 CDT)
Didn't Find vdw parameter QMMM McGuire, Kelly (Tue Mar 12 2019 - 21:41:31 CDT)
Research Programmer for VMD/NAMD at UIUC JoÃ£o Ribeiro (Tue Mar 12 2019 - 13:20:11 CDT)
Zero PME pencils found Alex Saad-Falcon (Tue Mar 12 2019 - 12:43:03 CDT)
Re: NAMD support for lone pairs Brian Radak (Tue Mar 12 2019 - 11:55:21 CDT)
Re: NAMD support for lone pairs Tabitha Nobel (Tue Mar 12 2019 - 11:11:39 CDT)
Re: NAMD support for lone pairs Gumbart, JC (Tue Mar 12 2019 - 08:35:03 CDT)
Re: NAMD support for lone pairs Brian Radak (Tue Mar 12 2019 - 07:50:44 CDT)
Re: Any NAMD-Working Small Organic Molecule Gumbart, JC (Mon Mar 11 2019 - 23:57:11 CDT)
Re: Colvars: implement a CV which requires computing minimal RMSDs with respect to multiple different reference frames yjcoshc (Mon Mar 11 2019 - 22:16:08 CDT)
Re: NAMD support for lone pairs Tabitha Nobel (Mon Mar 11 2019 - 20:01:06 CDT)
Any NAMD-Working Small Organic Molecule Alex Saad-Falcon (Mon Mar 11 2019 - 19:35:17 CDT)
Re: NAMD support for lone pairs Brian Radak (Mon Mar 11 2019 - 19:27:48 CDT)
Re: NAMD support for lone pairs Tabitha Nobel (Mon Mar 11 2019 - 18:10:43 CDT)
Re: NAMD support for lone pairs Brian Radak (Mon Mar 11 2019 - 17:38:33 CDT)
Re: NAMD support for lone pairs Tabitha Nobel (Mon Mar 11 2019 - 17:19:54 CDT)
Re: NAMD support for lone pairs Tabitha Nobel (Mon Mar 11 2019 - 17:15:45 CDT)
Re: NAMD support for lone pairs Brian Radak (Mon Mar 11 2019 - 16:39:24 CDT)
Re: NAMD support for lone pairs Brian Radak (Mon Mar 11 2019 - 16:30:56 CDT)
Re: NAMD support for lone pairs Tabitha Nobel (Mon Mar 11 2019 - 16:02:11 CDT)
Re: NAMD support for lone pairs Brian Radak (Mon Mar 11 2019 - 13:41:20 CDT)
Re: Colvars: implement a CV which requires computing minimal RMSDs with respect to multiple different reference frames Giacomo Fiorin (Mon Mar 11 2019 - 10:39:31 CDT)
Re: Colvars: implement a CV which requires computing minimal RMSDs with respect to multiple different reference frames yjcoshc_at_gmail.com (Mon Mar 11 2019 - 08:50:17 CDT)
Re: Colvars: implement a CV which requires computing minimal RMSDs with respect to multiple different reference frames JÃ©rÃ´me HÃ©nin (Mon Mar 11 2019 - 08:01:07 CDT)
Re: info about gpu hardware Stefano Guglielmo (Sun Mar 10 2019 - 03:38:15 CDT)
[namd] Help with sortreplicas Canal de Sebassen (Sat Mar 09 2019 - 13:01:49 CST)
Colvars: implement a CV which requires computing minimal RMSDs with respect to multiple different reference frames yjcoshc (Fri Mar 08 2019 - 19:41:00 CST)
Re: NAMD support for lone pairs Gumbart, JC (Fri Mar 08 2019 - 18:18:28 CST)
Re: NAMD support for lone pairs Brian Radak (Fri Mar 08 2019 - 14:14:36 CST)
Re: NAMD support for lone pairs Tabitha Nobel (Fri Mar 08 2019 - 11:10:13 CST)
Re: FATAL ERROR: Error in QM-MM bond assignment; bonded QM atoms with occupancy=1 Marcelo C. R. Melo (Fri Mar 08 2019 - 10:51:43 CST)
Re: Re: QM/MM error: The number of QM atoms received is different than expected Marcelo C. R. Melo (Fri Mar 08 2019 - 10:44:33 CST)
Re: NAMD support for lone pairs Brian Radak (Fri Mar 08 2019 - 09:45:39 CST)
NAMD support for lone pairs Tabitha Nobel (Thu Mar 07 2019 - 20:26:05 CST)
RE: NAMD Configuration file error Jim Phillips (Thu Mar 07 2019 - 11:13:51 CST)
Re: NAMD Configuration file error ê¹€ë¯¼ìž¬ (Thu Mar 07 2019 - 10:23:14 CST)
RE: NAMD Configuration file error Vermaas, Joshua (Thu Mar 07 2019 - 10:03:26 CST)
NAMD Configuration file error ê¹€ë¯¼ìž¬ (Thu Mar 07 2019 - 00:29:52 CST)
Re: QM/MM error: The number of QM atoms received is different than expected Haohao Fu (Wed Mar 06 2019 - 21:11:46 CST)
QM/MM error: The number of QM atoms received is different than expected Haohao Fu (Wed Mar 06 2019 - 21:08:27 CST)
RE: making new psf file from .prm and pdb file Vermaas, Joshua (Tue Mar 05 2019 - 21:01:40 CST)
making new psf file from .prm and pdb file Hadi Rahmaninejad (Tue Mar 05 2019 - 16:59:17 CST)
Re: Minimization Error ê¹€ë¯¼ìž¬ (Tue Mar 05 2019 - 05:02:52 CST)
Re: Minimization Error Pratik Narain Srivastava (Tue Mar 05 2019 - 01:01:22 CST)
Minimization Error ê¹€ë¯¼ìž¬ (Tue Mar 05 2019 - 00:31:36 CST)
Re: restrict atoms to cross a boundary Udaya Dahal (Mon Mar 04 2019 - 15:59:57 CST)
Re: restrict atoms to cross a boundary Giacomo Fiorin (Mon Mar 04 2019 - 15:50:04 CST)
restrict atoms to cross a boundary Udaya Dahal (Mon Mar 04 2019 - 13:42:09 CST)
FATAL ERROR: Error in QM-MM bond assignment; bonded QM atoms with occupancy=1 shreyas supekar (Mon Mar 04 2019 - 05:53:17 CST)
Re: Parameter Optimization Advice Roshan Shrestha (Fri Mar 01 2019 - 23:26:16 CST)
Re: Parameter Optimization Advice Gumbart, JC (Fri Mar 01 2019 - 23:22:28 CST)
Re: Parameter Optimization Advice Gumbart, JC (Fri Mar 01 2019 - 23:15:45 CST)
RE: "the error of movement of atoms" Vermaas, Joshua (Fri Mar 01 2019 - 16:21:35 CST)
Re: "the error of movement of atoms" Brian Radak (Fri Mar 01 2019 - 16:17:57 CST)
Re: Parameter Optimization Advice McGuire, Kelly (Fri Mar 01 2019 - 15:09:12 CST)
"the error of movement of atoms" soroush ziaei (Fri Mar 01 2019 - 11:33:21 CST)
Re: Parameter Optimization Advice Brian Radak (Fri Mar 01 2019 - 13:57:15 CST)
RE: Parameter Optimization Advice Vermaas, Joshua (Fri Mar 01 2019 - 13:54:23 CST)
Re: Parameter Optimization Advice McGuire, Kelly (Fri Mar 01 2019 - 13:42:39 CST)
RE: Parameter Optimization Advice Vermaas, Joshua (Fri Mar 01 2019 - 13:36:15 CST)
Re: Parameter Optimization Advice McGuire, Kelly (Fri Mar 01 2019 - 13:34:22 CST)
Re: Parameter Optimization Advice McGuire, Kelly (Fri Mar 01 2019 - 13:31:22 CST)
RE: Parameter Optimization Advice Lennart Nilsson (Fri Mar 01 2019 - 13:20:57 CST)
Re: Parameter Optimization Advice Brian Radak (Fri Mar 01 2019 - 13:18:15 CST)
Parameter Optimization Advice McGuire, Kelly (Fri Mar 01 2019 - 12:13:21 CST)
RE: Targeted molecular dynamics domain selection question Vermaas, Joshua (Fri Mar 01 2019 - 12:05:50 CST)
Re: Multiple Constraints Equilibration Giacomo Fiorin (Fri Mar 01 2019 - 11:56:53 CST)
Re: Multiple Constraints Equilibration Brian Radak (Fri Mar 01 2019 - 11:28:33 CST)
solvating silica Hadi Rahmaninejad (Fri Mar 01 2019 - 09:36:13 CST)
Multiple Constraints Equilibration McGuire, Kelly (Thu Feb 28 2019 - 19:30:52 CST)
RE: Targeted molecular dynamics domain selection question Vermaas, Joshua (Thu Feb 28 2019 - 18:52:29 CST)
Targeted molecular dynamics domain selection question Aditya Ranganathan (Thu Feb 28 2019 - 17:19:49 CST)
Re: strange benchmark results -- how would you explain them and what would you advice? Homeo Morphism (Thu Feb 28 2019 - 11:43:55 CST)
Re: Running NAMD on Linux Cluster ê¹€ë¯¼ìž¬ (Wed Feb 27 2019 - 18:45:34 CST)
Re: GolP-CHARMM horacio poblete (Wed Feb 27 2019 - 14:06:03 CST)
Re: Running NAMD on Linux Cluster Jim Phillips (Wed Feb 27 2019 - 13:57:49 CST)
Re: Running NAMD on Linux Cluster ê¹€ë¯¼ìž¬ (Wed Feb 27 2019 - 12:51:05 CST)
RE: Running NAMD on Linux Cluster Vermaas, Joshua (Wed Feb 27 2019 - 12:26:52 CST)
Re: Running NAMD on Linux Cluster Aravinda Munasinghe (Wed Feb 27 2019 - 12:03:35 CST)
GolP-CHARMM Mikhail Suyetin (Wed Feb 27 2019 - 10:24:21 CST)
Re: problem with solvating a structure Hadi Rahmaninejad (Wed Feb 27 2019 - 10:04:07 CST)
Fwd: Running NAMD on Linux Cluster ê¹€ë¯¼ìž¬ (Wed Feb 27 2019 - 07:10:34 CST)
AW: strange benchmark results -- how would you explain them and what would you advice? Norman Geist (Wed Feb 27 2019 - 04:57:12 CST)
Re: problem with solvating a structure Udaya Dahal (Tue Feb 26 2019 - 15:38:45 CST)
Re: problem with solvating a structure JoÃ£o Ribeiro (Tue Feb 26 2019 - 15:33:42 CST)
Re: problem with solvating a structure JoÃ£o Ribeiro (Tue Feb 26 2019 - 14:48:12 CST)
problem with solvating a structure Hadi Rahmaninejad (Tue Feb 26 2019 - 14:40:05 CST)
problem with solvating a structure Hadi Rahmaninejad (Tue Feb 26 2019 - 14:32:28 CST)
Re: Running NAMD on Linux Cluster Aravinda Munasinghe (Tue Feb 26 2019 - 14:06:13 CST)
patch for threonine (THP2). L- (Tue Feb 26 2019 - 12:46:15 CST)
strange benchmark results -- how would you explain them and what would you advice? Homeo Morphism (Tue Feb 26 2019 - 11:38:13 CST)
Running NAMD on Linux Cluster ê¹€ë¯¼ìž¬ (Tue Feb 26 2019 - 09:22:37 CST)
Re: colvar restraint simulation Prabir Khatua (Mon Feb 25 2019 - 13:52:39 CST)
Constant Force SMD Question McGuire, Kelly (Mon Feb 25 2019 - 12:25:34 CST)
Re: Stochastic velocity rescaling for Free Energy calculations Brian Radak (Mon Feb 25 2019 - 12:05:22 CST)
Re: colvar restraint simulation Giacomo Fiorin (Mon Feb 25 2019 - 11:40:17 CST)
RE: colvar restraint simulation Vermaas, Joshua (Mon Feb 25 2019 - 11:35:05 CST)
colvar restraint simulation Prabir Khatua (Mon Feb 25 2019 - 11:04:33 CST)
Re: Fwd: QM-MM NAMD-ORCA broken symmetry Marcelo C. R. Melo (Mon Feb 25 2019 - 10:23:20 CST)
Re: Fwd: QM-MM NAMD-ORCA broken symmetry Gerard Rowe (Mon Feb 25 2019 - 08:52:58 CST)
Stochastic velocity rescaling for Free Energy calculations Braden Kelly (Sat Feb 23 2019 - 15:21:37 CST)
Fwd: QM-MM NAMD-ORCA broken symmetry Francesco Pietra (Sat Feb 23 2019 - 14:34:22 CST)
Re: Lennard-Jones Potential Victor Kwan (Sat Feb 23 2019 - 12:41:34 CST)
Re: Lennard-Jones Potential McGuire, Kelly (Sat Feb 23 2019 - 12:11:08 CST)
Re: Lennard-Jones Potential Victor Kwan (Sat Feb 23 2019 - 12:09:01 CST)
Re: Lennard-Jones Potential McGuire, Kelly (Sat Feb 23 2019 - 12:02:18 CST)
Re: Lennard-Jones Potential Victor Kwan (Sat Feb 23 2019 - 12:00:36 CST)
H2 Topology and Parameter files Teja Vanjari (Sat Feb 23 2019 - 11:58:35 CST)
Re: Lennard-Jones Potential Kowsar Khajeh (Sat Feb 23 2019 - 11:47:11 CST)
Re: Lennard-Jones Potential McGuire, Kelly (Sat Feb 23 2019 - 11:37:58 CST)
Re: Lennard-Jones Potential Victor Kwan (Sat Feb 23 2019 - 11:35:49 CST)
Lennard-Jones Potential McGuire, Kelly (Sat Feb 23 2019 - 11:34:21 CST)
QM-MM NAMD-ORCA broken symmetry Francesco Pietra (Sat Feb 23 2019 - 10:38:42 CST)
Re: Constant Velocity Pulls McGuire, Kelly (Fri Feb 22 2019 - 13:12:56 CST)
Re: Constant Velocity Pulls Brian Radak (Fri Feb 22 2019 - 13:06:09 CST)
Re: Constant Velocity Pulls McGuire, Kelly (Fri Feb 22 2019 - 12:58:37 CST)
RE: Energy Minimization Simulation Vermaas, Joshua (Fri Feb 22 2019 - 12:55:37 CST)
RE: Constant Velocity Pulls Vermaas, Joshua (Fri Feb 22 2019 - 12:51:41 CST)
Energy Minimization Simulation ê¹€ë¯¼ìž¬ (Fri Feb 22 2019 - 12:09:38 CST)
Constant Velocity Pulls McGuire, Kelly (Fri Feb 22 2019 - 09:58:42 CST)
Re: Utilising the GPU in NAMD((NVIDIA CUDA acceleration) in windows Darin Lory (Thu Feb 21 2019 - 16:52:52 CST)
RE: Utilising the GPU in NAMD((NVIDIA CUDA acceleration) in windows Vermaas, Joshua (Thu Feb 21 2019 - 12:24:15 CST)
Re: Utilising the GPU in NAMD((NVIDIA CUDA acceleration) in windows Roessler, Bryan C (Thu Feb 21 2019 - 09:32:46 CST)
Utilising the GPU in NAMD((NVIDIA CUDA acceleration) in windows Denish Poudyal (Thu Feb 21 2019 - 08:59:29 CST)
Constant Velocity SMD Question McGuire, Kelly (Thu Feb 21 2019 - 01:32:02 CST)
Re: Running NAMD in MPI environment Jim Phillips (Wed Feb 20 2019 - 11:04:09 CST)
Running NAMD in MPI environment ê¹€ë¯¼ìž¬ (Wed Feb 20 2019 - 09:58:42 CST)
Re: Free energy plot Miao, Yinglong (Tue Feb 19 2019 - 21:34:04 CST)
Re: TIP4P water box Peter Freddolino (Tue Feb 19 2019 - 21:03:02 CST)
Re: Free energy plot Roshan Shrestha (Tue Feb 19 2019 - 19:31:12 CST)
Re: Running QM-MM multinode Francesco Pietra (Tue Feb 19 2019 - 14:25:32 CST)
TIP4P water box ê¹€ë¯¼ìž¬ (Tue Feb 19 2019 - 12:59:01 CST)
Free energy plot Faramarz Joodaki (Tue Feb 19 2019 - 11:57:20 CST)
Re: Running QM-MM multinode Gerard Rowe (Tue Feb 19 2019 - 11:25:59 CST)
Re: About restarting QM-MM simulation francesco.pietra_at_accademialucchese.it (Sun Feb 17 2019 - 15:50:41 CST)
Re: About restarting QM-MM simulation Marcelo C. R. Melo (Sun Feb 17 2019 - 15:26:12 CST)
Re: Running QM-MM multinode Francesco Pietra (Sun Feb 17 2019 - 01:41:05 CST)
Re: Error running deinterleave_idws.py on FEP simulation output Brian Radak (Sat Feb 16 2019 - 13:18:44 CST)
Re: Running QM-MM multinode Bennion, Brian (Sat Feb 16 2019 - 12:03:19 CST)
Running QM-MM multinode Francesco Pietra (Sat Feb 16 2019 - 02:12:26 CST)
Re: Error running deinterleave_idws.py on FEP simulation output Amy Rice (Fri Feb 15 2019 - 16:13:04 CST)
Re: About restarting QM-MM simulation Francesco Pietra (Fri Feb 15 2019 - 02:34:56 CST)
Re: vmd-l: PDB structures of peptides Aravinda Munasinghe (Thu Feb 14 2019 - 18:26:40 CST)
Re: About restarting QM-MM simulation Francesco Pietra (Thu Feb 14 2019 - 16:34:46 CST)
Re: QMMM Question McGuire, Kelly (Thu Feb 14 2019 - 14:06:11 CST)
Re: QMMM Question Brian Radak (Thu Feb 14 2019 - 13:04:50 CST)
Re: Dual topology FEP for anions Brian Radak (Thu Feb 14 2019 - 12:11:47 CST)
Re: About restarting QM-MM simulation Marcelo C. R. Melo (Thu Feb 14 2019 - 11:33:24 CST)
QMMM Question McGuire, Kelly (Thu Feb 14 2019 - 11:26:53 CST)
Re: About restarting QM-MM simulation Gerard Rowe (Thu Feb 14 2019 - 10:38:06 CST)
RE: Dual topology FEP for anions Vermaas, Joshua (Thu Feb 14 2019 - 09:59:17 CST)
Re: About restarting QM-MM simulation Francesco Pietra (Thu Feb 14 2019 - 08:46:34 CST)
Re: About restarting QM-MM simulation Francesco Pietra (Thu Feb 14 2019 - 04:17:35 CST)
PDB structures of peptides Mikhail Suyetin (Thu Feb 14 2019 - 03:05:15 CST)
Dual topology FEP for anions Hristina Zhekova (Wed Feb 13 2019 - 18:57:12 CST)
Re: About restarting QM-MM simulation Marcelo C. R. Melo (Wed Feb 13 2019 - 16:20:33 CST)
solute scaling does not affect electrostatics (and other quirks) Jeff Comer (Wed Feb 13 2019 - 15:20:02 CST)
Re: About restarting QM-MM simulation Francesco Pietra (Wed Feb 13 2019 - 14:47:45 CST)
Re: About restarting QM-MM simulation Francesco Pietra (Wed Feb 13 2019 - 14:47:13 CST)
Re: Force constant for Umbrella sampling and WHAM Udaya Dahal (Wed Feb 13 2019 - 13:08:44 CST)
Re: About restarting QM-MM simulation Eric Smoll (Wed Feb 13 2019 - 12:48:05 CST)
Error running deinterleave_idws.py on FEP simulation output Amy Rice (Wed Feb 13 2019 - 12:42:10 CST)
Re: About restarting QM-MM simulation Marcelo C. R. Melo (Wed Feb 13 2019 - 12:31:57 CST)
RE: Force constant for Umbrella sampling and WHAM Vermaas, Joshua (Wed Feb 13 2019 - 12:24:51 CST)
Re: Force constant for Umbrella sampling and WHAM Giacomo Fiorin (Wed Feb 13 2019 - 12:19:47 CST)
Force constant for Umbrella sampling and WHAM Udaya Dahal (Wed Feb 13 2019 - 12:07:42 CST)
About restarting QM-MM simulation Francesco Pietra (Wed Feb 13 2019 - 09:32:54 CST)
Re: Gromacs to Charmm FF Format Conversion -Reg Mani Kandan (Tue Feb 12 2019 - 10:40:15 CST)
Re: CSVR + eABF, system temperature set to zero Michael von Domaros (Tue Feb 12 2019 - 16:38:01 CST)
RE: Gromacs to Charmm FF Format Conversion -Reg Vermaas, Joshua (Tue Feb 12 2019 - 10:34:53 CST)
Re: Large number of simulations in parallel using replica exchange. Brian Radak (Tue Feb 12 2019 - 10:32:28 CST)
Re: info about gpu hardware Roessler, Bryan C (Tue Feb 12 2019 - 09:47:57 CST)
Fwd: Gromacs to Charmm FF Format Conversion -Reg Mani Kandan (Tue Feb 12 2019 - 09:44:10 CST)
RE: Gromacs to Charmm FF Format Conversion -Reg Lennart Nilsson (Tue Feb 12 2019 - 09:40:18 CST)
Re: Gromacs to Charmm FF Format Conversion -Reg Roessler, Bryan C (Tue Feb 12 2019 - 09:23:28 CST)
Gromacs to Charmm FF Format Conversion -Reg Mani Kandan (Tue Feb 12 2019 - 08:12:40 CST)
Re: CSVR + eABF, system temperature set to zero Giacomo Fiorin (Tue Feb 12 2019 - 07:19:53 CST)
AW: Large number of simulations in parallel using replica exchange. Norman Geist (Tue Feb 12 2019 - 01:54:14 CST)
Re: CSVR + eABF, system temperature set to zero Giacomo Fiorin (Mon Feb 11 2019 - 22:15:47 CST)
Re: Large number of simulations in parallel using replica exchange. Giacomo Fiorin (Mon Feb 11 2019 - 22:06:38 CST)
Re: Large number of simulations in parallel using replica exchange. Aravinda Munasinghe (Mon Feb 11 2019 - 21:44:41 CST)
Re: Sending REUS simulations to Stampede Canal de Sebassen (Mon Feb 11 2019 - 21:25:31 CST)
Re: Sending REUS simulations to Stampede Giacomo Fiorin (Mon Feb 11 2019 - 21:02:55 CST)
Sending REUS simulations to Stampede Canal de Sebassen (Mon Feb 11 2019 - 19:39:24 CST)
CSVR + eABF, system temperature set to zero Michael von Domaros (Mon Feb 11 2019 - 18:51:37 CST)
Large number of simulations in parallel using replica exchange. Dipak Balasaheb Sanap (Mon Feb 11 2019 - 14:52:26 CST)
Re: Maximum Timestep for NAMD Prakash Saud (Sun Feb 10 2019 - 09:59:51 CST)
Re: jeevan gc (Sun Feb 10 2019 - 09:52:26 CST)
Re: Using harmonic walls on water molecules Moises Ernesto Romero (Fri Feb 08 2019 - 15:23:45 CST)
Re: Maximum Timestep for NAMD Aravinda Munasinghe (Fri Feb 08 2019 - 09:07:55 CST)
Re: reinitatoms Brian Radak (Fri Feb 08 2019 - 07:51:25 CST)
Re: reinitatoms Laura Lopes (Fri Feb 08 2019 - 03:38:55 CST)
AW: MSM grid values Norman Geist (Fri Feb 08 2019 - 03:04:28 CST)
AW: MSM grid values Norman Geist (Fri Feb 08 2019 - 02:59:55 CST)
Re: MSM grid values Denish Poudyal (Thu Feb 07 2019 - 19:46:23 CST)
Re: Maximum Timestep for NAMD Giacomo Fiorin (Thu Feb 07 2019 - 15:57:46 CST)
Re: Maximum Timestep for NAMD Giacomo Fiorin (Thu Feb 07 2019 - 15:37:58 CST)
Re: Maximum Timestep for NAMD Braden Kelly (Thu Feb 07 2019 - 15:34:48 CST)
RE: Maximum Timestep for NAMD Vermaas, Joshua (Thu Feb 07 2019 - 15:02:20 CST)
Re: Maximum Timestep for NAMD Richard Overstreet (Thu Feb 07 2019 - 14:51:30 CST)
Re: MSM grid values David Hardy (Thu Feb 07 2019 - 14:43:02 CST)
RE: Maximum Timestep for NAMD Bennion, Brian (Thu Feb 07 2019 - 14:41:57 CST)
Maximum Timestep for NAMD Alex Saad-Falcon (Thu Feb 07 2019 - 14:24:30 CST)
MSM grid values Denish Poudyal (Wed Feb 06 2019 - 23:15:24 CST)
RE: Using harmonic walls on water molecules Vermaas, Joshua (Mon Feb 04 2019 - 19:50:52 CST)
Using harmonic walls on water molecules Moises Ernesto Romero (Mon Feb 04 2019 - 19:14:39 CST)
Re: Tuning QM-MM with namd-orca on one cluster node Francesco Pietra (Mon Feb 04 2019 - 01:54:31 CST)
Re: Tuning QM-MM with namd-orca on one cluster node Marcelo C. R. Melo (Sun Feb 03 2019 - 17:03:54 CST)
Fwd: Tuning QM-MM with namd-orca on one cluster node Francesco Pietra (Sat Feb 02 2019 - 03:07:47 CST)
Re: Tuning QM-MM with namd-orca on one cluster node Francesco Pietra (Fri Feb 01 2019 - 09:24:44 CST)
Re: Fwd: Tuning QM-MM with namd-orca on one cluster node Francesco Pietra (Fri Feb 01 2019 - 09:10:40 CST)
Re: Tuning QM-MM with namd-orca on one cluster node Marcelo C. R. Melo (Thu Jan 31 2019 - 16:41:35 CST)
Re: Fwd: Tuning QM-MM with namd-orca on one cluster node Jim Phillips (Thu Jan 31 2019 - 15:47:35 CST)
Fwd: Tuning QM-MM with namd-orca on one cluster node Francesco Pietra (Thu Jan 31 2019 - 15:30:40 CST)
Re: Tuning QM-MM with namd-orca on one cluster node Francesco Pietra (Thu Jan 31 2019 - 15:22:25 CST)
RE: info about gpu hardware Vermaas, Joshua (Thu Jan 31 2019 - 13:35:54 CST)
Re: Tuning QM-MM with namd-orca on one cluster node Marcelo C. R. Melo (Thu Jan 31 2019 - 13:07:53 CST)
Tuning QM-MM with namd-orca on one cluster node Francesco Pietra (Thu Jan 31 2019 - 12:25:15 CST)
info about gpu hardware Stefano Guglielmo (Thu Jan 31 2019 - 11:12:57 CST)
Re: pre compiled charmm-6.8.2 for namd2.13 nightly version compilation for multiple GPU node simulations Aravinda Munasinghe (Thu Jan 31 2019 - 08:58:00 CST)
Re: pre compiled charmm-6.8.2 for namd2.13 nightly version compilation for multiple GPU node simulations Giacomo Fiorin (Thu Jan 31 2019 - 08:50:46 CST)
Re: pre compiled charmm-6.8.2 for namd2.13 nightly version compilation for multiple GPU node simulations Aravinda Munasinghe (Wed Jan 30 2019 - 20:18:13 CST)
Re: Question about colvars Faramarz Joodaki (Wed Jan 30 2019 - 19:29:31 CST)
RE: Question about colvars Vermaas, Joshua (Wed Jan 30 2019 - 19:19:56 CST)
Question about colvars Faramarz Joodaki (Wed Jan 30 2019 - 19:06:12 CST)
Re: pre compiled charmm-6.8.2 for namd2.13 nightly version compilation for multiple GPU node simulations Aravinda Munasinghe (Wed Jan 30 2019 - 17:17:56 CST)
Re: pre compiled charmm-6.8.2 for namd2.13 nightly version compilation for multiple GPU node simulations Jim Phillips (Wed Jan 30 2019 - 16:34:39 CST)
Re: pre compiled charmm-6.8.2 for namd2.13 nightly version compilation for multiple GPU node simulations Aravinda Munasinghe (Tue Jan 29 2019 - 22:32:06 CST)
RE: pre compiled charmm-6.8.2 for namd2.13 nightly version compilation for multiple GPU node simulations Vermaas, Joshua (Tue Jan 29 2019 - 11:42:29 CST)
pre compiled charmm-6.8.2 for namd2.13 nightly version compilation for multiple GPU node simulations Aravinda Munasinghe (Tue Jan 29 2019 - 10:37:15 CST)
Re: hbond restraint simulation Prabir Khatua (Mon Jan 28 2019 - 15:40:36 CST)
RE: hbond restraint simulation Vermaas, Joshua (Mon Jan 28 2019 - 15:23:57 CST)
RE: "-nan" free energy from WHAM analysis Vermaas, Joshua (Mon Jan 28 2019 - 09:37:24 CST)
Re: gaussian aMD with iE=2 (setting E threshold at maximum) Vlad Cojocaru (Mon Jan 28 2019 - 09:26:31 CST)
Re: gaussian aMD with iE=2 (setting E threshold at maximum) Miao, Yinglong (Mon Jan 28 2019 - 09:02:37 CST)
Re: hbond restraint simulation Prabir Khatua (Sun Jan 27 2019 - 16:33:59 CST)
"-nan" free energy from WHAM analysis Junwoong Yoon (Sun Jan 27 2019 - 12:11:58 CST)
Re: gaussian aMD with iE=2 (setting E threshold at maximum) Vlad Cojocaru (Sun Jan 27 2019 - 06:00:02 CST)
RE: run MD simulation in NAMD using stages file strategy or allin one file ? soroush ziaei (Sat Jan 26 2019 - 14:26:04 CST)
Re: gaussian aMD with iE=2 (setting E threshold at maximum) Miao, Yinglong (Sat Jan 26 2019 - 13:23:41 CST)
Re: run MD simulation in NAMD using stages file strategy or all in one file ? L- (Sat Jan 26 2019 - 10:59:20 CST)
Re: jeevan gc (Sat Jan 26 2019 - 09:45:22 CST)
RE: hbond restraint simulation Vermaas, Joshua (Fri Jan 25 2019 - 16:01:31 CST)
RE: Phosphotyrosine Parameters/Toplogy Lennart Nilsson (Fri Jan 25 2019 - 14:35:51 CST)
RE: hbond restraint simulation Vermaas, Joshua (Fri Jan 25 2019 - 14:09:52 CST)
RE: Phosphotyrosine Parameters/Toplogy Vermaas, Joshua (Fri Jan 25 2019 - 13:57:26 CST)
hbond restraint simulation Prabir Khatua (Fri Jan 25 2019 - 13:19:24 CST)
Phosphotyrosine Parameters/Toplogy Alex Saad-Falcon (Fri Jan 25 2019 - 12:10:14 CST)
RE: Vermaas, Joshua (Fri Jan 25 2019 - 11:59:35 CST)
gaussian aMD with iE=2 (setting E threshold at maximum) Vlad Cojocaru (Fri Jan 25 2019 - 07:32:43 CST)
Re: AW: restarting Gaussian accelerated MD fails Vlad Cojocaru (Fri Jan 25 2019 - 04:48:50 CST)
Re: restarting Gaussian accelerated MD fails Vlad Cojocaru (Fri Jan 25 2019 - 04:11:03 CST)
(no subject) jeevan gc (Thu Jan 24 2019 - 16:53:46 CST)
Re: restarting Gaussian accelerated MD fails Miao, Yinglong (Tue Jan 22 2019 - 14:10:21 CST)
Re: mdff for EM map with helical symmetry and the asymmetric unit is dimer Ryan McGreevy (Tue Jan 22 2019 - 14:07:55 CST)
Re: restarting Gaussian accelerated MD fails Vlad Cojocaru (Tue Jan 22 2019 - 02:56:58 CST)
Modifying LJ Potential -Reg Mani Kandan (Sat Jan 19 2019 - 22:24:07 CST)
Re: Angle list Ashkan Shekaari (Sat Jan 19 2019 - 09:19:00 CST)
RE: Angle list soroush ziaei (Sat Jan 19 2019 - 08:55:27 CST)
Angle list Ashkan Shekaari (Sat Jan 19 2019 - 07:49:35 CST)
Re: RE: FATAL ERROR with "File exists" Seibold, Steve Allan (Fri Jan 18 2019 - 09:37:24 CST)
mdff for EM map with helical symmetry and the asymmetric unit is dimer Zhang Yan (Thu Jan 17 2019 - 21:28:37 CST)
Re: RE: FATAL ERROR with "File exists" Zhang Yan (Thu Jan 17 2019 - 21:16:17 CST)
RE: RE: FATAL ERROR with "File exists" Vermaas, Joshua (Thu Jan 17 2019 - 12:36:28 CST)
RE: Graphene psf file soroush ziaei (Thu Jan 17 2019 - 08:23:01 CST)
Re: RE: FATAL ERROR with "File exists" Zhang Yan (Wed Jan 16 2019 - 21:03:57 CST)
pre compiled namd2.13 version nightly build for Linux-x86_64-verbs-smp-CUDA or help with compiling charm++ Aravinda Munasinghe (Wed Jan 16 2019 - 20:16:26 CST)
RE: FATAL ERROR with "File exists" Vermaas, Joshua (Wed Jan 16 2019 - 13:51:51 CST)
FATAL ERROR with "File exists" Seibold, Steve Allan (Wed Jan 16 2019 - 12:30:48 CST)
Re: Several issues (possible bugs) in REST2 - soluteScalingFile & langevinTemp Jim Phillips (Tue Jan 15 2019 - 16:57:42 CST)
Several issues (possible bugs) in REST2 - soluteScalingFile & langevinTemp Aravinda Munasinghe (Tue Jan 15 2019 - 15:31:04 CST)
QM-MM and transition elements Francesco Pietra (Tue Jan 15 2019 - 11:20:39 CST)
mistakes in the user guide in the accelerated MD section ? Vlad Cojocaru (Tue Jan 15 2019 - 07:29:02 CST)
Re: [External] running NAMD with Slurm Jim Phillips (Mon Jan 14 2019 - 14:29:55 CST)
Re: Graphene psf file Victor Kwan (Mon Jan 14 2019 - 13:42:06 CST)
Re: Extracting velocities from veldcd file Prakash Saud (Mon Jan 14 2019 - 07:46:51 CST)
Re: Extracting velocities from veldcd file Roshan Shrestha (Mon Jan 14 2019 - 07:36:39 CST)
Extracting velocities from veldcd file ARNAB MUKHERJEE (Mon Jan 14 2019 - 07:01:09 CST)
Graphene psf file Ashkan Shekaari (Wed Jan 09 2019 - 13:14:03 CST)
Re: [External] running NAMD with Slurm Bennion, Brian (Wed Jan 09 2019 - 12:56:14 CST)
Re: [External] running NAMD with Slurm Seibold, Steve Allan (Wed Jan 09 2019 - 12:52:44 CST)
Re: [External] running NAMD with Slurm Sharp, Kim (Wed Jan 09 2019 - 12:41:20 CST)
Re: running NAMD with Slurm on cluster Victor Kwan (Wed Jan 09 2019 - 12:05:07 CST)
Re: [External] running NAMD with Slurm Bennion, Brian (Wed Jan 09 2019 - 11:57:54 CST)
Re: [External] running NAMD with Slurm Sharp, Kim (Wed Jan 09 2019 - 11:15:19 CST)
running NAMD with Slurm Seibold, Steve Allan (Wed Jan 09 2019 - 09:54:21 CST)
Re: [External] running NAMD with Slurm on cluster Sharp, Kim (Wed Jan 09 2019 - 09:30:32 CST)
running NAMD with Slurm on cluster Seibold, Steve Allan (Wed Jan 09 2019 - 09:08:57 CST)
Re: CHARMM force field for Hydrogen bond? Ashkan Shekaari (Tue Jan 08 2019 - 13:58:19 CST)
Re: Running QM-MM MOPAC on a cluster Francesco Pietra (Tue Jan 08 2019 - 11:06:27 CST)
Re: CHARMM force field for Hydrogen bond? HEMANTH H 18310019 (Mon Jan 07 2019 - 20:59:58 CST)
CHARMM force field for Hydrogen bond? Nasim Rajabi (Mon Jan 07 2019 - 16:15:43 CST)
Re: Error in using the QMElecEmbed keyword Marcelo C. R. Melo (Mon Jan 07 2019 - 13:07:28 CST)
Re: Wrong result in running QM/MM simulation with a small test system Marcelo C. R. Melo (Mon Jan 07 2019 - 12:55:52 CST)
Re: Running QM-MM MOPAC on a cluster Jim Phillips (Mon Jan 07 2019 - 10:40:56 CST)
Re: Protein Charge Brian Radak (Mon Jan 07 2019 - 10:39:28 CST)
Re: Protein Charge Peter Freddolino (Mon Jan 07 2019 - 10:17:32 CST)
Re: Protein Charge Ashkan Shekaari (Mon Jan 07 2019 - 07:42:25 CST)
RE: Protein Charge soroush ziaei (Mon Jan 07 2019 - 07:37:06 CST)
Protein Charge Ashkan Shekaari (Mon Jan 07 2019 - 02:24:15 CST)
Re: unable to open restart.colvars Giacomo Fiorin (Fri Jan 04 2019 - 13:10:26 CST)
Re: Running QM-MM MOPAC on a cluster Francesco Pietra (Fri Jan 04 2019 - 12:28:32 CST)
Error in using the QMElecEmbed keyword Xi Chen (Fri Jan 04 2019 - 12:13:58 CST)
Re: unable to open restart.colvars Francesco Pietra (Fri Jan 04 2019 - 11:16:08 CST)
Wrong result in running QM/MM simulation with a small test system Xi Chen (Thu Jan 03 2019 - 20:17:29 CST)
Re: unable to open restart.colvars Giacomo Fiorin (Thu Jan 03 2019 - 13:57:50 CST)
Re: unable to open restart.colvars Victor Kwan (Thu Jan 03 2019 - 13:19:20 CST)
Re: ERROR: Constraint failure in RATTLE algorithm for atom 232! ERROR: Constraint failure; simulation has become unstable. Roshan Shrestha (Thu Jan 03 2019 - 01:08:21 CST)
ERROR: Constraint failure in RATTLE algorithm for atom 232! ERROR: Constraint failure; simulation has become unstable. Denish Poudyal (Wed Jan 02 2019 - 23:48:59 CST)
Re: Running QM-MM MOPAC on a cluster Jim Phillips (Wed Jan 02 2019 - 16:40:46 CST)
CG simulation of water molecules -Reg Mani Kandan (Wed Jan 02 2019 - 14:06:46 CST)
Re: QM-MM with MOPAC Marcelo C. R. Melo (Wed Jan 02 2019 - 09:33:25 CST)
Re: Running QM-MM MOPAC on a cluster Francesco Pietra (Tue Jan 01 2019 - 03:24:43 CST)
Re: Running QM-MM MOPAC on a cluster Jim Phillips (Mon Dec 31 2018 - 09:42:27 CST)
unable to open restart.colvars Francesco Pietra (Mon Dec 31 2018 - 01:47:21 CST)
QM-MM with MOPAC Francesco Pietra (Mon Dec 31 2018 - 01:32:04 CST)
Coarse Grained simulation of silicon nitride nanopore - Reg Mani Kandan (Fri Dec 28 2018 - 13:35:58 CST)
Error in NAMD Simulations -Drude HEMANTH H 18310019 (Mon Dec 24 2018 - 00:24:23 CST)
Re: Running QM-MM MOPAC on a cluster Francesco Pietra (Fri Dec 21 2018 - 13:17:13 CST)
RE: What NAMD version to obtain Vermaas, Joshua (Wed Dec 19 2018 - 17:14:33 CST)
Re: What NAMD version to obtain Renfro, Michael (Wed Dec 19 2018 - 15:08:37 CST)
What NAMD version to obtain Seibold, Steve Allan (Wed Dec 19 2018 - 14:35:12 CST)
Re: How to add a C code to NAMD properly? Giacomo Fiorin (Wed Dec 19 2018 - 13:45:21 CST)
Re: Running QM-MM MOPAC on a cluster Jim Phillips (Tue Dec 18 2018 - 16:03:22 CST)
Re: How to add a C code to NAMD properly? Faramarz Joodaki (Tue Dec 18 2018 - 09:37:25 CST)
Re: Running QM-MM MOPAC on a cluster Francesco Pietra (Mon Dec 17 2018 - 15:22:11 CST)
MOPAC Plugin Update McGuire, Kelly (Mon Dec 17 2018 - 14:01:13 CST)
Re: Running QM-MM MOPAC on a cluster Jim Phillips (Mon Dec 17 2018 - 09:12:25 CST)
Re: How to add a C code to NAMD properly? Giacomo Fiorin (Sun Dec 16 2018 - 22:36:26 CST)
Fwd: Question on restraints with MM-GBSA Francesco Pietra (Sun Dec 16 2018 - 13:28:47 CST)
Re: How to add a C code to NAMD properly? Faramarz Joodaki (Sun Dec 16 2018 - 11:59:19 CST)
Re: How to add a C code to NAMD properly? Faramarz Joodaki (Sun Dec 16 2018 - 11:50:41 CST)
Question on restraints with MM-GBSA Francesco Pietra (Sun Dec 16 2018 - 04:47:36 CST)
Re: Running QM-MM MOPAC on a cluster Francesco Pietra (Sun Dec 16 2018 - 01:47:41 CST)
Re: How to add a C code to NAMD properly? yjcoshc_at_gmail.com (Sat Dec 15 2018 - 19:33:28 CST)
Re: Running QM-MM MOPAC on a cluster Jim Phillips (Fri Dec 14 2018 - 09:29:51 CST)
Running QM-MM MOPAC on a cluster Francesco Pietra (Fri Dec 14 2018 - 04:21:04 CST)
Re: Constant Force Pull McGuire, Kelly (Thu Dec 13 2018 - 10:33:13 CST)
run MD simulation in NAMD using stages file strategy or all in one file ? L- (Thu Dec 13 2018 - 10:12:13 CST)
Constant Force Pull McGuire, Kelly (Thu Dec 13 2018 - 03:44:18 CST)
RE: Wrapping multimeric protein issues Vermaas, Joshua (Wed Dec 12 2018 - 18:10:57 CST)
Wrapping multimeric protein issues Jacob Usadi (Wed Dec 12 2018 - 17:51:55 CST)
Re: User force field with FEP? Giacomo Fiorin (Tue Dec 11 2018 - 14:16:10 CST)
Re: User force field with FEP? Brian Radak (Tue Dec 11 2018 - 14:02:12 CST)
Re: User force field with FEP? Randy J. Zauhar (Tue Dec 11 2018 - 14:01:04 CST)
Re: User force field with FEP? Giacomo Fiorin (Tue Dec 11 2018 - 13:44:33 CST)
User force field with FEP? Randy J. Zauhar (Tue Dec 11 2018 - 13:27:00 CST)
Re: C36 force field Ashkan Shekaari (Tue Dec 11 2018 - 11:21:24 CST)
Re: C36 force field Ashkan Shekaari (Tue Dec 11 2018 - 11:16:31 CST)
Re: C36 force field JoÃ£o Ribeiro (Tue Dec 11 2018 - 10:55:00 CST)
Re: C36 force field JoÃ£o Ribeiro (Tue Dec 11 2018 - 09:23:31 CST)
Re: C36 force field HEMANTH H 18310019 (Tue Dec 11 2018 - 08:41:47 CST)
C36 force field Ashkan Shekaari (Tue Dec 11 2018 - 07:34:38 CST)
RE: problems running GPU-accelerated namd Vermaas, Joshua (Mon Dec 10 2018 - 12:10:06 CST)
Re: Regarding free energy Brian Radak (Mon Dec 10 2018 - 11:47:27 CST)
Re: problems running GPU-accelerated namd Victor Kwan (Mon Dec 10 2018 - 09:14:02 CST)
Regarding free energy Abhishek Kumar Singh (Sun Dec 09 2018 - 22:30:57 CST)
Re: problems running GPU-accelerated namd Renfro, Michael (Sun Dec 09 2018 - 10:07:21 CST)
problems running GPU-accelerated namd æŽè€€ (Sun Dec 09 2018 - 02:02:36 CST)
RE: Parallel Jobs Vermaas, Joshua (Thu Dec 06 2018 - 15:21:18 CST)
Re: Parallel Jobs Renfro, Michael (Thu Dec 06 2018 - 15:05:19 CST)
Re: Parallel Jobs Bennion, Brian (Thu Dec 06 2018 - 15:01:48 CST)
Re: Parallel Jobs McGuire, Kelly (Thu Dec 06 2018 - 14:54:30 CST)
Re: Parallel Jobs Bennion, Brian (Thu Dec 06 2018 - 14:51:38 CST)
Parallel Jobs McGuire, Kelly (Thu Dec 06 2018 - 14:36:45 CST)
Re: NAMD compiling problem Faramarz Joodaki (Thu Dec 06 2018 - 14:08:52 CST)
Re: NAMD compiling problem Giacomo Fiorin (Thu Dec 06 2018 - 11:12:27 CST)
Re: NAMD compiling problem Giacomo Fiorin (Thu Dec 06 2018 - 11:11:25 CST)
NAMD compiling problem Faramarz Joodaki (Thu Dec 06 2018 - 10:59:17 CST)
Re: tar.gz incorrect firmat? Francesco Pietra (Thu Dec 06 2018 - 02:58:05 CST)
Re: How to add a C code to NAMD properly? Faramarz Joodaki (Wed Dec 05 2018 - 19:51:57 CST)
Re: How to add a C code to NAMD properly? yjcoshc (Wed Dec 05 2018 - 19:45:11 CST)
Re: How to add a C code to NAMD properly? Faramarz Joodaki (Wed Dec 05 2018 - 18:39:07 CST)
Re: tar.gz incorrect firmat? Darin Lory (Wed Dec 05 2018 - 15:01:08 CST)
tar.gz incorrect firmat? Francesco Pietra (Wed Dec 05 2018 - 14:51:50 CST)
Re: ERROR TOLERANCE L- (Wed Dec 05 2018 - 14:00:47 CST)
Re: ERROR TOLERANCE Giacomo Fiorin (Wed Dec 05 2018 - 13:51:42 CST)
ERROR TOLERANCE L- (Wed Dec 05 2018 - 13:32:42 CST)
Positive energy for protein Ashkan Shekaari (Mon Dec 03 2018 - 08:20:58 CST)
Reg Membrane simulation Vidhya Sankar (Mon Dec 03 2018 - 07:43:58 CST)
Positive energy values for protein Ashkan Shekaari (Sat Dec 01 2018 - 07:43:48 CST)
Water Transport McGuire, Kelly (Thu Nov 29 2018 - 13:34:54 CST)
Re: How to add a C code to NAMD properly? yjcoshc (Tue Nov 27 2018 - 19:44:25 CST)
Re: How to add a C code to NAMD properly? Faramarz Joodaki (Tue Nov 27 2018 - 16:10:46 CST)
Re: NAMD QM/MM alchemical free energy change capabilities? Brian Radak (Tue Nov 27 2018 - 08:26:34 CST)
NAMD QM/MM alchemical free energy change capabilities? Braden Kelly (Mon Nov 26 2018 - 22:07:33 CST)
Re: [ REST2 ] Possible bug on NAMD example Jim Phillips (Mon Nov 26 2018 - 11:19:57 CST)
Re: How to add a C code to NAMD properly? yjcoshc (Sat Nov 24 2018 - 19:20:22 CST)
How to add a C code to NAMD properly? Faramarz Joodaki (Fri Nov 23 2018 - 12:58:39 CST)
Magnetic field Ashkan Shekaari (Thu Nov 22 2018 - 07:22:46 CST)
[ REST2 ] Possible bug on NAMD example Diego Gomes (Thu Nov 22 2018 - 07:06:41 CST)
NAMD 2.13 and RTX2080Ti Battocchio, Giovanni (Thu Nov 22 2018 - 06:52:57 CST)
RE: Problems about constraint (conskcol) in umbrella sampling conf file Vermaas, Joshua (Wed Nov 21 2018 - 11:46:56 CST)
Problems about constraint (conskcol) in umbrella sampling conf file æŽè€€ (Wed Nov 21 2018 - 09:44:53 CST)
Re: [NAMD] Running REUS in many nodes The Cromicus Productions (Tue Nov 20 2018 - 18:40:55 CST)
RE: [NAMD] Running REUS in many nodes Vermaas, Joshua (Tue Nov 20 2018 - 16:51:32 CST)
[NAMD] Running REUS in many nodes The Cromicus Productions (Tue Nov 20 2018 - 16:12:01 CST)
Re: Is there a problem of ORCA running for NAMD MPI? Marcelo C. R. Melo (Tue Nov 20 2018 - 11:21:58 CST)
Re: Is there a problem of ORCA running for NAMD MPI? Francesco Pietra (Tue Nov 20 2018 - 09:32:34 CST)
Re: Is there a problem of ORCA running for NAMD MPI? Gerard Rowe (Tue Nov 20 2018 - 08:12:49 CST)
Is there a problem of ORCA running for NAMD MPI? Francesco Pietra (Tue Nov 20 2018 - 03:35:17 CST)
Re: NAMD/VMD installation for Windows 10 Fotis Baltoumas (Mon Nov 19 2018 - 10:59:48 CST)
NAMD/VMD installation for Windows 10 Joey Gehring (Mon Nov 19 2018 - 10:27:22 CST)
Fwd: Running QM-MM tutorial on a cluster Francesco Pietra (Sun Nov 18 2018 - 00:44:44 CST)
Running QM-MM tutorial on a cluster Francesco Pietra (Sat Nov 17 2018 - 13:30:02 CST)
Re: ffTK torsion scan convergence using Gaussian. Dipak Balasaheb Sanap (Tue Nov 13 2018 - 20:14:40 CST)
Re: ffTK torsion scan convergence using Gaussian. Dipak Balasaheb Sanap (Tue Nov 13 2018 - 20:07:02 CST)
Re: ffTK torsion scan convergence using Gaussian. Gumbart, James C (Tue Nov 13 2018 - 20:04:59 CST)
Re: ffTK torsion scan convergence using Gaussian. Gumbart, James C (Tue Nov 13 2018 - 19:56:23 CST)
Re: Unusual WT-Metadynamics gaussians heights Giacomo Fiorin (Tue Nov 13 2018 - 13:50:47 CST)
Re: Unusual WT-Metadynamics gaussians heights Bruno Cuevas ZuvirÃa (Tue Nov 13 2018 - 10:16:51 CST)
Re: Minimization Question McGuire, Kelly (Tue Nov 13 2018 - 09:39:49 CST)
Re: Minimization Question Gerard Rowe (Tue Nov 13 2018 - 07:54:53 CST)
Re: Unusual WT-Metadynamics gaussians heights Giacomo Fiorin (Tue Nov 13 2018 - 07:44:58 CST)
Re: Minimization Question McGuire, Kelly (Mon Nov 12 2018 - 20:52:19 CST)
Re: Minimization Question Brian Radak (Mon Nov 12 2018 - 20:41:26 CST)
Re: Minimization Question McGuire, Kelly (Mon Nov 12 2018 - 19:50:51 CST)
ffTK torsion scan convergence using Gaussian. Dipak Balasaheb Sanap (Mon Nov 12 2018 - 18:08:12 CST)
Re: Minimization Question McGuire, Kelly (Mon Nov 12 2018 - 15:37:01 CST)
Re: Minimization Question McGuire, Kelly (Mon Nov 12 2018 - 15:35:57 CST)
Re: Minimization Question Brian Radak (Mon Nov 12 2018 - 13:45:43 CST)
Re: FEP Rattle Error Ebru Ã‡etin (Mon Nov 12 2018 - 13:30:08 CST)
Re: Minimization Question Gerard Rowe (Mon Nov 12 2018 - 13:08:00 CST)
Re: FEP Rattle Error Brian Radak (Mon Nov 12 2018 - 12:11:41 CST)
Re: Setting alchElecLambdaStart 1.0 parameter for FEP calculations Brian Radak (Mon Nov 12 2018 - 12:01:45 CST)
RE: Building with GCC on Ubuntu 18 Vermaas, Joshua (Mon Nov 12 2018 - 11:34:11 CST)
Re: Building with GCC on Ubuntu 18 Jim Phillips (Mon Nov 12 2018 - 09:08:30 CST)
Unusual WT-Metadynamics gaussians heights Bruno Cuevas ZuvirÃa (Mon Nov 12 2018 - 04:25:08 CST)
Minimization Question McGuire, Kelly (Sun Nov 11 2018 - 19:46:19 CST)
FEP Rattle Error Ebru Ã‡etin (Sun Nov 11 2018 - 17:07:51 CST)
Re: Concatenate Outputs McGuire, Kelly (Sat Nov 10 2018 - 14:52:45 CST)
RE: CHARMM36 parameters for nucelobases Lennart Nilsson (Sat Nov 10 2018 - 10:57:04 CST)
RE: CHARMM36 parameters for nucelobases Lennart Nilsson (Sat Nov 10 2018 - 10:24:29 CST)
Re: CHARMM36 parameters for nucelobases HEMANTH H 18310019 (Sat Nov 10 2018 - 07:14:49 CST)
CHARMM36 parameters for nucelobases Shivangi Nangia (Sat Nov 10 2018 - 07:03:34 CST)
RE: Building with GCC on Ubuntu 18 Jim Phillips (Fri Nov 09 2018 - 16:17:41 CST)
Concatenate Outputs McGuire, Kelly (Fri Nov 09 2018 - 14:12:21 CST)
RE: Building with GCC on Ubuntu 18 Vermaas, Joshua (Fri Nov 09 2018 - 12:42:37 CST)
Setting alchElecLambdaStart 1.0 parameter for FEP calculations David Huggins (Fri Nov 09 2018 - 12:08:51 CST)
Using center of mass to calculate the radial distribution function Yi Lun Lee (Fri Nov 09 2018 - 11:37:36 CST)
Re: Way to wget or curl download the precompiled NAMD? Darin Lory (Fri Nov 09 2018 - 10:02:09 CST)
Re: Way to wget or curl download the precompiled NAMD? Jim Phillips (Fri Nov 09 2018 - 09:31:17 CST)
Re: Way to wget or curl download the precompiled NAMD? Darin Lory (Thu Nov 08 2018 - 16:19:33 CST)
RE: Way to wget or curl download the precompiled NAMD? Vermaas, Joshua (Thu Nov 08 2018 - 15:37:21 CST)
Way to wget or curl download the precompiled NAMD? Darin Lory (Thu Nov 08 2018 - 15:13:22 CST)
Re: creating topology for a unique structure soroush ziaei (Thu Nov 08 2018 - 14:29:17 CST)
RE: Building with GCC on Ubuntu 18 Vermaas, Joshua (Thu Nov 08 2018 - 11:50:54 CST)
Re: Building with GCC on Ubuntu 18 Julio Maia (Thu Nov 08 2018 - 11:26:36 CST)
Re: creating topology for a unique structure Brian Radak (Thu Nov 08 2018 - 09:55:53 CST)
creating topology for a unique structure soroush ziaei (Wed Nov 07 2018 - 11:05:08 CST)
Re: Binding free energy tutorial Gumbart, James C (Wed Nov 07 2018 - 12:16:06 CST)
Re: Binding free energy tutorial Nassar, Omneya (Wed Nov 07 2018 - 08:56:56 CST)
Re: Binding free energy tutorial jing liang (Wed Nov 07 2018 - 08:17:44 CST)
Re: QM/MM Question McGuire, Kelly (Tue Nov 06 2018 - 15:52:41 CST)
Re: QM/MM Question McGuire, Kelly (Tue Nov 06 2018 - 13:40:14 CST)
Re: Langevin Dynamics Coefficient Value -Reg Brian Radak (Tue Nov 06 2018 - 13:34:00 CST)
Re: QM/MM Question Gerard Rowe (Tue Nov 06 2018 - 13:17:42 CST)
Langevin Dynamics Coefficient Value -Reg Mani Kandan (Tue Nov 06 2018 - 11:30:09 CST)
Re: QM/MM Question McGuire, Kelly (Mon Nov 05 2018 - 21:23:11 CST)
Re: QM/MM Question Gerard Rowe (Mon Nov 05 2018 - 16:19:08 CST)
Re: Error with D-amino acids mid-sequence using NAMD 2.12/2.13b2 and CHARMm36 Gumbart, James C (Mon Nov 05 2018 - 14:17:46 CST)
Re: QM/MM Question McGuire, Kelly (Mon Nov 05 2018 - 13:46:39 CST)
Re: QM/MM Question Gerard Rowe (Mon Nov 05 2018 - 13:41:11 CST)
Re: Error with D-amino acids mid-sequence using NAMD 2.12/2.13b2 and CHARMm36 Giacomo Fiorin (Mon Nov 05 2018 - 13:13:06 CST)
Re: QM/MM Question McGuire, Kelly (Mon Nov 05 2018 - 12:14:02 CST)
RE: Gaussian Dihedral Scan Log files visualization. Vermaas, Joshua (Mon Nov 05 2018 - 12:10:48 CST)
Re: Error with D-amino acids mid-sequence using NAMD 2.12/2.13b2 and CHARMm36 Giacomo Fiorin (Mon Nov 05 2018 - 11:36:47 CST)
Re: Error with D-amino acids mid-sequence using NAMD 2.12/2.13b2 and CHARMm36 Brian Radak (Mon Nov 05 2018 - 11:18:56 CST)
Re: QM/MM Question McGuire, Kelly (Mon Nov 05 2018 - 11:13:45 CST)
Re: creating topology for a unique structure Brian Radak (Mon Nov 05 2018 - 10:49:48 CST)
Error with D-amino acids mid-sequence using NAMD 2.12/2.13b2 and CHARMm36 Travis Hesketh (Mon Nov 05 2018 - 10:04:49 CST)
Re: QM/MM Question Gerard Rowe (Mon Nov 05 2018 - 07:32:06 CST)
Re: NVIDIA Quadro(R) GV100 card for NAMD studies Giacomo Fiorin (Mon Nov 05 2018 - 07:29:48 CST)
QM/MM Question McGuire, Kelly (Sun Nov 04 2018 - 12:59:51 CST)
Re: Fix aminoacids - error Abhishek TYAGI (Sun Nov 04 2018 - 06:33:55 CST)
Fix aminoacids - error Villalain Boullon, Jose (Sun Nov 04 2018 - 03:18:23 CST)
creating topology for a unique structure soroush ziaei (Sun Nov 04 2018 - 02:02:03 CST)
Gaussian Dihedral Scan Log files visualization. Dipak Balasaheb Sanap (Sat Nov 03 2018 - 21:47:47 CDT)
qmSecProc Proper Use McGuire, Kelly (Fri Nov 02 2018 - 15:02:00 CDT)
Re: Re: ORCA GPUs Julio Maia (Fri Nov 02 2018 - 13:13:21 CDT)
Re: ORCA GPUs McGuire, Kelly (Fri Nov 02 2018 - 13:04:20 CDT)
Re: ORCA GPUs McGuire, Kelly (Fri Nov 02 2018 - 12:58:08 CDT)
Re: ORCA GPUs Gerard Rowe (Fri Nov 02 2018 - 12:56:39 CDT)
Re: Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately? Brian Radak (Fri Nov 02 2018 - 09:28:21 CDT)
Re: ORCA GPUs Gerard Rowe (Fri Nov 02 2018 - 09:14:41 CDT)
Re: Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately? Asghar Razavi (Fri Nov 02 2018 - 08:30:21 CDT)
Re: NVIDIA Quadro(R) GV100 card for NAMD studies sesha surya vara prasad reddy karri (Fri Nov 02 2018 - 07:05:04 CDT)
Re: NVIDIA Quadro(R) GV100 card for NAMD studies Giacomo Fiorin (Fri Nov 02 2018 - 06:48:30 CDT)
NVIDIA Quadro(R) GV100 card for NAMD studies sesha surya vara prasad reddy karri (Fri Nov 02 2018 - 05:58:41 CDT)
ORCA GPUs McGuire, Kelly (Thu Nov 01 2018 - 20:48:47 CDT)
Re: ORCA QMMM McGuire, Kelly (Thu Nov 01 2018 - 20:46:10 CDT)
detecting vanishing atoms in zero.fep soroush ziaei (Thu Nov 01 2018 - 18:03:12 CDT)
Re: detecting vanishing atoms in zero.fep Brian Radak (Thu Nov 01 2018 - 16:59:58 CDT)
Re: ORCA QMMM Gerard Rowe (Thu Nov 01 2018 - 16:26:34 CDT)
Re: Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately? Peter Freddolino (Thu Nov 01 2018 - 15:45:16 CDT)
detecting vanishing atoms in zero.fep soroush ziaei (Thu Nov 01 2018 - 15:39:07 CDT)
Re: ORCA QMMM McGuire, Kelly (Thu Nov 01 2018 - 14:45:51 CDT)
Re: ORCA QMMM McGuire, Kelly (Thu Nov 01 2018 - 14:42:34 CDT)
Re: Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately? Nielsen, Steven (Thu Nov 01 2018 - 12:30:21 CDT)
Is there really no way of automating pair interaction calculations without invoking NAMD for each pdb file separately? Asghar Razavi (Thu Nov 01 2018 - 11:43:30 CDT)
Re: bpti example compiled source charmrun++ does not launch Jim Phillips (Thu Nov 01 2018 - 11:33:45 CDT)
Re: bpti example compiled source charmrun++ does not launch Renfro, Michael (Thu Nov 01 2018 - 10:14:24 CDT)
bpti example compiled source charmrun++ does not launch Hazard, E. Starr (Thu Nov 01 2018 - 09:31:05 CDT)
Re: FFtK Tutorial (Urey-Bradley angles error). Jim Phillips (Thu Nov 01 2018 - 01:31:51 CDT)
Re: Couldn't open DCD file Jim Phillips (Wed Oct 31 2018 - 15:33:06 CDT)
Couldn't open DCD file Hazard, E. Starr (Wed Oct 31 2018 - 14:19:30 CDT)
RE: Membrane Simulation Vermaas, Joshua (Wed Oct 31 2018 - 12:49:17 CDT)
Re: Membrane Simulation Jim Phillips (Wed Oct 31 2018 - 12:15:59 CDT)
Re: FFtK Tutorial (Urey-Bradley angles error). JoÃ£o Ribeiro (Wed Oct 31 2018 - 12:05:35 CDT)
Re: detecting vanishing atoms in zero.fep Brian Radak (Wed Oct 31 2018 - 09:06:15 CDT)
Re: Binding free energy tutorial jing liang (Wed Oct 31 2018 - 04:31:13 CDT)
Membrane Simulation Alice Zheng (Tue Oct 30 2018 - 20:58:03 CDT)
Re: QM/MM Error McGuire, Kelly (Tue Oct 30 2018 - 12:43:50 CDT)
Re: QM/MM Error Marcelo C. R. Melo (Tue Oct 30 2018 - 12:15:42 CDT)
Re: ORCA QMMM McGuire, Kelly (Tue Oct 30 2018 - 09:46:11 CDT)
RE: parameter request for PRES bonding Lennart Nilsson (Tue Oct 30 2018 - 09:31:59 CDT)
Re: parameter request for PRES bonding Francesco Pietra (Tue Oct 30 2018 - 09:16:39 CDT)
Re: ORCA QMMM Gerard Rowe (Tue Oct 30 2018 - 07:42:20 CDT)
ORCA QMMM McGuire, Kelly (Mon Oct 29 2018 - 17:41:25 CDT)
Re: parameter request for PRES bonding Gumbart, James C (Mon Oct 29 2018 - 13:07:40 CDT)
Re: parameter request for PRES bonding Francesco Pietra (Mon Oct 29 2018 - 02:07:38 CDT)
QM/MM Error McGuire, Kelly (Mon Oct 29 2018 - 00:01:25 CDT)
QM/MM Question McGuire, Kelly (Sun Oct 28 2018 - 21:53:59 CDT)
RE: parameter request for PRES bonding Vermaas, Joshua (Sun Oct 28 2018 - 18:09:06 CDT)
Re: Binding free energy tutorial David Hardy (Sun Oct 28 2018 - 11:47:37 CDT)
Re: detecting vanishing atoms in zero.fep Brian Radak (Sun Oct 28 2018 - 10:39:22 CDT)
Re: Alchdecouple for dihedral/improper terms Brian Radak (Sun Oct 28 2018 - 10:34:04 CDT)
Re: Binding free energy tutorial Giacomo Fiorin (Sun Oct 28 2018 - 10:20:50 CDT)
detecting vanishing atoms in zero.fep soroush ziaei (Sat Oct 27 2018 - 16:37:20 CDT)
Re: Binding free energy tutorial David Hardy (Sat Oct 27 2018 - 15:34:24 CDT)
Alchdecouple for dihedral/improper terms David Huggins (Sat Oct 27 2018 - 10:21:26 CDT)
Re: David Hardy (Sat Oct 27 2018 - 04:22:03 CDT)
Re: Binding free energy tutorial David Hardy (Sat Oct 27 2018 - 03:15:30 CDT)
Fwd: parameter request for PRES bonding Francesco Pietra (Sat Oct 27 2018 - 02:29:39 CDT)
parameter request for PRES bonding Francesco Pietra (Sat Oct 27 2018 - 02:27:05 CDT)
Binding free energy tutorial jing liang (Fri Oct 26 2018 - 14:37:51 CDT)
FFtK Tutorial (Urey-Bradley angles error). Dipak Balasaheb Sanap (Fri Oct 26 2018 - 14:20:59 CDT)
(no subject) Darin Lory (Fri Oct 26 2018 - 11:22:41 CDT)
Equilibration of membrane water system (pressure in NVT) Rene Hamburger UNI KL (Fri Oct 26 2018 - 02:32:38 CDT)
RE: Positive VDW energies Vermaas, Joshua (Thu Oct 25 2018 - 18:29:47 CDT)
Re: Positive VDW energies Giacomo Fiorin (Thu Oct 25 2018 - 16:32:50 CDT)
Positive VDW energies Nick Palmer (Thu Oct 25 2018 - 14:54:58 CDT)
Re: Standard density -reg Mani Kandan (Wed Oct 24 2018 - 23:30:55 CDT)
Re: Nano-bio interaction in NAMD Jeff Comer (Wed Oct 24 2018 - 16:23:33 CDT)
Re: multi-node mpiexec issue Jim Phillips (Wed Oct 24 2018 - 16:08:40 CDT)
Re: adaptive biasing force Jeff Comer (Wed Oct 24 2018 - 16:00:02 CDT)
Re: Standard density -reg Jeff Comer (Wed Oct 24 2018 - 15:50:32 CDT)
adaptive biasing force Artur Hermano (Wed Oct 24 2018 - 14:08:35 CDT)
Standard density -reg Mani Kandan (Wed Oct 24 2018 - 02:07:44 CDT)
re: Nano-bio interaction in NAMD fhh2626 (Tue Oct 23 2018 - 10:22:52 CDT)
Nano-bio interaction in NAMD Ashkan Shekaari (Tue Oct 23 2018 - 10:01:09 CDT)
RE: error in (runfepmin) Vermaas, Joshua (Mon Oct 22 2018 - 13:51:10 CDT)
Re: error in (runfepmin) HEMANTH H 18310019 (Sun Oct 21 2018 - 23:13:26 CDT)
error in (runfepmin) soroush ziaei (Sun Oct 21 2018 - 18:02:24 CDT)
Surface Tension calculation Yi Lun Lee (Fri Oct 19 2018 - 15:33:58 CDT)
Re: git rid of it David Hardy (Fri Oct 19 2018 - 15:17:49 CDT)
Re: constant temprature for vacuum condition in namd file Giacomo Fiorin (Fri Oct 19 2018 - 14:26:48 CDT)
git rid of it Scott Brozell (Fri Oct 19 2018 - 14:21:57 CDT)
constant temprature for vacuum condition in namd file soroush ziaei (Fri Oct 19 2018 - 14:19:53 CDT)
RE: vacuum condition in config file Vermaas, Joshua (Fri Oct 19 2018 - 14:08:18 CDT)
vacuum condition in config file soroush ziaei (Fri Oct 19 2018 - 13:58:37 CDT)
Re: ABF Window Boundaries Giacomo Fiorin (Fri Oct 19 2018 - 10:35:27 CDT)
Re: ABF Window Boundaries McGuire, Kelly (Fri Oct 19 2018 - 10:34:38 CDT)
Re: ABF Window Boundaries McGuire, Kelly (Fri Oct 19 2018 - 10:32:41 CDT)
ABF Window Boundaries McGuire, Kelly (Fri Oct 19 2018 - 02:45:07 CDT)
Re: the fep error in third part of config file Brian Radak (Thu Oct 18 2018 - 15:10:31 CDT)
Re: the fep error in third part of config file soroush ziaei (Thu Oct 18 2018 - 04:13:08 CDT)
Re: Colvars and distance restraint for umbrella sampling Udaya Dahal (Wed Oct 17 2018 - 10:58:13 CDT)
Re: Colvars and distance restraint for umbrella sampling Gumbart, James C (Wed Oct 17 2018 - 10:49:11 CDT)
Re: Colvars and distance restraint for umbrella sampling Udaya Dahal (Wed Oct 17 2018 - 10:41:00 CDT)
Re: Colvars and distance restraint for umbrella sampling Gumbart, James C (Wed Oct 17 2018 - 10:27:01 CDT)
Fwd: the fep error in third part of config file Brian Radak (Wed Oct 17 2018 - 09:14:48 CDT)
Re: Colvars and distance restraint for umbrella sampling Udaya Dahal (Tue Oct 16 2018 - 19:41:21 CDT)
Re: Colvars and distance restraint for umbrella sampling Giacomo Fiorin (Tue Oct 16 2018 - 19:31:15 CDT)
Colvars and distance restraint for umbrella sampling Udaya Dahal (Tue Oct 16 2018 - 19:08:07 CDT)
Re: Affinity David Hardy (Tue Oct 16 2018 - 17:27:30 CDT)
Affinity Mahmood Naderan (Tue Oct 16 2018 - 15:20:52 CDT)
Re: the fep error in third part of config file Brian Radak (Mon Oct 15 2018 - 14:17:23 CDT)
RE: Calculating hydrophilic and hydrophobic Solvent Accessible Surface Area Vermaas, Joshua (Mon Oct 15 2018 - 10:35:25 CDT)
Calculating hydrophilic and hydrophobic Solvent Accessible Surface Area Rabeta Yeasmin (Mon Oct 15 2018 - 10:26:45 CDT)
the fep error in third part of config file soroush ziaei (Mon Oct 15 2018 - 09:50:25 CDT)
Re: the instance type selection for NAMD simulation in Amason marketplace Ryan McGreevy (Mon Oct 15 2018 - 08:45:31 CDT)
the instance type selection for NAMD simulation in Amason marketplace sunyeping (Mon Oct 15 2018 - 07:09:54 CDT)
Re: E-field to Voltage - Reg Mani Kandan (Fri Oct 05 2018 - 21:49:03 CDT)
Re: E-field to Voltage - Reg Bassam Haddad (Fri Oct 05 2018 - 14:57:54 CDT)
Re: Setting up QM/MM calculations with QwikMD without the GUI JoÃ£o Ribeiro (Fri Oct 05 2018 - 13:44:31 CDT)
Re: E-field to Voltage - Reg Mani Kandan (Fri Oct 05 2018 - 12:40:26 CDT)
Re: E-field to Voltage - Reg Giacomo Fiorin (Fri Oct 05 2018 - 11:43:51 CDT)
Setting up QM/MM calculations with QwikMD without the GUI Agisilaos Chantzis (Fri Oct 05 2018 - 11:20:54 CDT)
E-field to Voltage - Reg Mani Kandan (Fri Oct 05 2018 - 09:58:19 CDT)
Temperature Fluctuations in Drude Simulations - NAMD HEMANTH H 18310019 (Thu Oct 04 2018 - 23:39:14 CDT)
g++ 5.3 fails on 2.12/2.13b1 with CUDA 8.0 Chris Borchert (Thu Oct 04 2018 - 15:59:10 CDT)
Re: How to simulate flexible water with TIP4P potential? Brian Radak (Wed Oct 03 2018 - 16:46:21 CDT)
Re: How to simulate flexible water with TIP4P potential? Alfonso GijÃ³n (Wed Oct 03 2018 - 13:13:59 CDT)
Re: How to simulate flexible water with TIP4P potential? David Hardy (Wed Oct 03 2018 - 10:35:58 CDT)
Re: How to simulate flexible water with TIP4P potential? Brian Radak (Wed Oct 03 2018 - 09:34:42 CDT)
How to simulate flexible water with TIP4P potential? Alfonso GijÃ³n (Wed Oct 03 2018 - 08:15:12 CDT)
RE: Mismatch in atom number between psf and dcd files Wintrode, Patrick (Mon Oct 01 2018 - 14:11:24 CDT)
Diffusion Coefficient calculation Kinkini Jayasundara (Fri Sep 28 2018 - 20:48:39 CDT)
RE: Mismatch in atom number between psf and dcd files Vermaas, Joshua (Fri Sep 28 2018 - 11:23:05 CDT)
Re: SWM4-NDP PSF File David Hardy (Fri Sep 28 2018 - 10:35:46 CDT)
Mismatch in atom number between psf and dcd files Wintrode, Patrick (Fri Sep 28 2018 - 10:04:11 CDT)
Re: SWM4-NDP PSF File Brian Radak (Thu Sep 27 2018 - 21:22:26 CDT)
Re: SWM4-NDP PSF File David Hardy (Thu Sep 27 2018 - 18:07:09 CDT)
Re: SWM4-NDP PSF File Brian Radak (Thu Sep 27 2018 - 08:41:10 CDT)
SWM4-NDP PSF File Julian MÃ¼ller (Thu Sep 27 2018 - 02:48:10 CDT)
ABF Question McGuire, Kelly (Wed Sep 26 2018 - 21:32:54 CDT)
RE: About CUDA version Vermaas, Joshua (Tue Sep 25 2018 - 15:06:54 CDT)
Re: About CUDA version Mahmood Naderan (Tue Sep 25 2018 - 14:43:33 CDT)
Re: About CUDA version Bassam Haddad (Tue Sep 25 2018 - 14:04:14 CDT)
About CUDA version Mahmood Naderan (Tue Sep 25 2018 - 13:22:21 CDT)
RE: PBC error. Amber force field in NAMD Vermaas, Joshua (Tue Sep 25 2018 - 11:35:42 CDT)
PBC error. Amber force field in NAMD M RCC (Tue Sep 25 2018 - 06:35:53 CDT)
First "Hands-On" Workshop on Structural DNA Nanotechnology JoÃ£o Ribeiro (Mon Sep 24 2018 - 09:13:30 CDT)
Critical isofrom selectivity in molecular dynamics M RCC (Mon Sep 24 2018 - 06:23:14 CDT)
Re: Constraint failure in Highly charged system - Reg Mani Kandan (Sun Sep 23 2018 - 23:23:50 CDT)
AW: Bad structure after converting the coarse grained last frame to all-atom Norman Geist (Fri Sep 21 2018 - 01:08:00 CDT)
Constraint failure in Highly charged system - Reg Mani Kandan (Thu Sep 20 2018 - 23:33:16 CDT)
Re: Bad structure after converting the coarse grained last frame to all-atom Peter Freddolino (Thu Sep 20 2018 - 11:14:35 CDT)
Re: calculating non bonded energy using namdenergy Peter Freddolino (Thu Sep 20 2018 - 11:13:50 CDT)
Re: Bad structure after converting the coarse grained last frame to all-atom Rabeta Yeasmin (Thu Sep 20 2018 - 09:58:39 CDT)
Re: calculating non bonded energy using namdenergy Giacomo Fiorin (Thu Sep 20 2018 - 09:49:14 CDT)
RE: Best water model Vermaas, Joshua (Thu Sep 20 2018 - 08:50:50 CDT)
Best water model ê¹€ë¯¼ìž¬ (Thu Sep 20 2018 - 07:54:34 CDT)
calculating non bonded energy using namdenergy Monika Madhavi (Wed Sep 19 2018 - 22:19:16 CDT)
Re: Bad structure after converting the coarse grained last frame to all-atom Peter Freddolino (Wed Sep 19 2018 - 20:52:15 CDT)
Re: Bad structure after converting the coarse grained last frame to all-atom Rabeta Yeasmin (Wed Sep 19 2018 - 13:00:29 CDT)
Re: Do firsttimestep, numsteps and run have maximum values? David Hardy (Wed Sep 19 2018 - 10:04:28 CDT)
Re: Do firsttimestep, numsteps and run have maximum values? yjcoshc_at_gmail.com (Wed Sep 19 2018 - 09:52:56 CDT)
Re: Do firsttimestep, numsteps and run have maximum values? Brian Radak (Wed Sep 19 2018 - 09:32:29 CDT)
Do firsttimestep, numsteps and run have maximum values? yjcoshc (Tue Sep 18 2018 - 20:42:05 CDT)
Re: Bad structure after converting the coarse grained last frame to all-atom Rabeta Yeasmin (Tue Sep 18 2018 - 13:36:40 CDT)
Re: Bad structure after converting the coarse grained last frame to all-atom Peter Freddolino (Tue Sep 18 2018 - 12:26:59 CDT)
Re: Bad structure after converting the coarse grained last frame to all-atom Rabeta Yeasmin (Tue Sep 18 2018 - 10:58:25 CDT)
Re: Right NAMD version Giacomo Fiorin (Tue Sep 18 2018 - 08:19:50 CDT)
Right NAMD version Fidan Sumbul (Tue Sep 18 2018 - 06:00:36 CDT)
Re: Bad structure after converting the coarse grained last frame to all-atom Peter Freddolino (Mon Sep 17 2018 - 15:58:31 CDT)
Bad structure after converting the coarse grained last frame to all-atom Rabeta Yeasmin (Mon Sep 17 2018 - 11:50:49 CDT)
Re: Different cell vectors - Reg Axel Kohlmeyer (Mon Sep 17 2018 - 05:09:27 CDT)
Re: Different cell vectors - Reg Mani Kandan (Mon Sep 17 2018 - 04:56:25 CDT)
Re: Different cell vectors - Reg Axel Kohlmeyer (Mon Sep 17 2018 - 04:49:10 CDT)
Different cell vectors - Reg Mani Kandan (Mon Sep 17 2018 - 04:45:10 CDT)
Re: Using 4-site water model in NAMD Nassar, Omneya (Sun Sep 16 2018 - 22:35:57 CDT)
Re: Using 4-site water model in NAMD Haohao Fu (Sun Sep 16 2018 - 22:20:33 CDT)
Re: Using 4-site water model in NAMD Peter Freddolino (Sun Sep 16 2018 - 22:11:44 CDT)
Re: Using 4-site water model in NAMD Nassar, Omneya (Sun Sep 16 2018 - 22:05:37 CDT)
Re: Using 4-site water model in NAMD Nassar, Omneya (Sun Sep 16 2018 - 22:04:00 CDT)
Using 4-site water model in NAMD Haohao Fu (Sun Sep 16 2018 - 20:05:23 CDT)
Re: regarding umbrella sampling simulation Nassar, Omneya (Fri Sep 14 2018 - 23:47:27 CDT)
regarding umbrella sampling simulation san kumar (Fri Sep 14 2018 - 23:11:54 CDT)
Re: Ewald size-dependence correction in FEP simulation of an electric dipole Brian Radak (Fri Sep 14 2018 - 09:37:16 CDT)
Re: Ewald size-dependence correction in FEP simulation of an electric dipole Nassar, Omneya (Fri Sep 14 2018 - 08:02:04 CDT)
Re: Ewald size-dependence correction in FEP simulation of an electric dipole Nassar, Omneya (Fri Sep 14 2018 - 07:47:39 CDT)
RE: Ewald size-dependence correction in FEP simulation of an electric dipole Nassar, Omneya (Thu Sep 13 2018 - 21:54:08 CDT)
Reg membrane hydration Vidhya Sankar (Thu Sep 13 2018 - 21:01:39 CDT)
Re: Ewald size-dependence correction in FEP simulation of an electric dipole Victor Kwan (Thu Sep 13 2018 - 10:57:31 CDT)
RE: Ewald size-dependence correction in FEP simulation of an electric dipole Nassar, Omneya (Wed Sep 12 2018 - 23:16:02 CDT)
Ewald size-dependence correction in FEP simulation of an electric dipole Ali Mehdizadeh Rahimi (Wed Sep 12 2018 - 19:34:37 CDT)
Re: vmd-l: Enhanced Sampling and Free-Energy Calculations Lectures JoÃ£o Ribeiro (Wed Sep 12 2018 - 08:56:28 CDT)
Re: Cutoff radius for electrostatic embedding in QM/MM calculations Agisilaos Chantzis (Mon Sep 10 2018 - 12:41:25 CDT)
Enhanced Sampling and Free-Energy Calculations Lectures JoÃ£o Ribeiro (Mon Sep 10 2018 - 12:02:42 CDT)
Re: Cutoff radius for electrostatic embedding in QM/MM calculations Marcelo C. R. Melo (Mon Sep 10 2018 - 11:53:13 CDT)
Re: Re: namd simulation input file setting from NPT to NVT Giacomo Fiorin (Mon Sep 10 2018 - 11:25:54 CDT)
Re: namd simulation input file setting from NPT to NVT Yi Lun Lee (Mon Sep 10 2018 - 11:19:14 CDT)
Need help preventing hydration of the lipid-protein interface Vidhya Sankar (Mon Sep 10 2018 - 07:38:50 CDT)
Need help preventing hydration of the lipid-protein using tcl script Vidhya Sankar (Mon Sep 10 2018 - 07:34:34 CDT)
Re: Rattle algorithm Constraint failure - Reg David Hardy (Fri Sep 07 2018 - 09:31:19 CDT)
Rattle algorithm Constraint failure - Reg Mani Kandan (Fri Sep 07 2018 - 05:46:59 CDT)
RE: namd simulation input file setting from NPT to NVT Vermaas, Joshua (Thu Sep 06 2018 - 16:04:20 CDT)
namd simulation input file setting from NPT to NVT Yi Lun Lee (Thu Sep 06 2018 - 15:31:10 CDT)
Cutoff radius for electrostatic embedding in QM/MM calculations Agisilaos Chantzis (Wed Sep 05 2018 - 10:21:23 CDT)
Re: energy calculation with namdenergy Brian Radak (Wed Sep 05 2018 - 08:18:56 CDT)
Re: Unexpected Energy values - Reg Brian Radak (Wed Sep 05 2018 - 08:15:40 CDT)
energy calculation with namdenergy Monika Madhavi (Wed Sep 05 2018 - 07:32:00 CDT)
Unexpected Energy values - Reg Mani Kandan (Wed Sep 05 2018 - 07:07:29 CDT)
Re: parameter file for ACE and CT3 cap JoÃ£o Ribeiro (Tue Sep 04 2018 - 08:02:57 CDT)
Re: parameter file for ACE and CT3 cap Dhiraj Srivastava (Mon Sep 03 2018 - 11:59:40 CDT)
Re: parameter file for ACE and CT3 cap Victor Kwan (Mon Sep 03 2018 - 11:52:35 CDT)
parameter file for ACE and CT3 cap Dhiraj Srivastava (Sun Sep 02 2018 - 19:45:14 CDT)
multi-node mpiexec issue Ryuzo Azuma (Fri Aug 31 2018 - 11:44:26 CDT)
Re: Re: Error NPT simulation - Need Urgent Help - Reg Brian Radak (Fri Aug 31 2018 - 09:22:48 CDT)
Re: Error NPT simulation - Need Urgent Help - Reg Mani Kandan (Fri Aug 31 2018 - 08:38:44 CDT)
AW: Weird PBC wrapping Norman Geist (Fri Aug 31 2018 - 01:58:11 CDT)
Re: Weird PBC wrapping Giacomo Fiorin (Thu Aug 30 2018 - 08:41:54 CDT)
Weird PBC wrapping Michail Lazaratos (Thu Aug 30 2018 - 05:41:11 CDT)
Re: Error NPT simulation - Need Urgent Help - Reg David Hardy (Wed Aug 29 2018 - 12:01:46 CDT)
Error NPT simulation - Need Urgent Help - Reg Mani Kandan (Wed Aug 29 2018 - 11:35:02 CDT)
Re: Question: constant-pH to standard MD Brian Radak (Fri Aug 24 2018 - 10:16:30 CDT)
Question: constant-pH to standard MD Yasser Bruno Ruiz Blanco (Fri Aug 24 2018 - 02:34:43 CDT)
Re: CGenFF 4.1 lone pairs Brian Radak (Wed Aug 22 2018 - 17:37:57 CDT)
CGenFF 4.1 lone pairs Jeff Comer (Wed Aug 22 2018 - 13:56:30 CDT)
Re: Three bonds with water in vmd from NAMD DCD Natalia Ostrowska (Wed Aug 22 2018 - 04:27:42 CDT)
Re: Three bonds with water in vmd from NAMD DCD Giacomo Fiorin (Tue Aug 21 2018 - 10:04:42 CDT)
Three bonds with water in vmd from NAMD DCD Seibold, Steve Allan (Tue Aug 21 2018 - 09:17:43 CDT)
Re: ERROR in multiple walker metadynamics simulation Brian Radak (Tue Aug 21 2018 - 09:05:31 CDT)
ERROR in multiple walker metadynamics simulation Miyu Tamura (Tue Aug 21 2018 - 01:30:09 CDT)
Re: MOPAC Point Charges Marcelo C. R. Melo (Mon Aug 20 2018 - 16:40:46 CDT)
Re: FEP atom velocity. Brian Radak (Mon Aug 20 2018 - 13:15:01 CDT)
MOPAC Point Charges Gerard Rowe (Mon Aug 20 2018 - 12:29:36 CDT)
FEP atom velocity. Aashish Bhatt (Mon Aug 20 2018 - 01:10:35 CDT)
Induced Electric filed and Electrostatics - Reg Mani Kandan (Sun Aug 19 2018 - 02:54:45 CDT)
RE: FATAL ERROR: Unable to access config file temp14.conf Vermaas, Joshua (Fri Aug 17 2018 - 13:15:46 CDT)
FATAL ERROR: Unable to access config file temp14.conf Charles Hoying (Thu Aug 16 2018 - 20:44:17 CDT)
Converting a mixture system from NAMD to LAMMPS Sonibare, Kolawole (Thu Aug 16 2018 - 12:14:56 CDT)
Re: QM/MM MD and the qmParamPDB file Agisilaos Chantzis (Thu Aug 16 2018 - 04:25:56 CDT)
Re: QM/MM MD and the qmParamPDB file Marcelo C. R. Melo (Wed Aug 15 2018 - 22:43:27 CDT)
AW: AW: AW: Periodic cell has become too small for original patch grid Norman Geist (Wed Aug 15 2018 - 09:52:28 CDT)
AW: AW: AW: Periodic cell has become too small for original patch grid Norman Geist (Wed Aug 15 2018 - 09:52:13 CDT)
QM/MM MD and the qmParamPDB file Agisilaos Chantzis (Wed Aug 15 2018 - 07:48:40 CDT)
Re: AW: AW: Periodic cell has become too small for original patch grid Rohit Modee (Wed Aug 15 2018 - 06:06:12 CDT)
AW: AW: Periodic cell has become too small for original patch grid Norman Geist (Wed Aug 15 2018 - 05:52:38 CDT)
Re: AW: Periodic cell has become too small for original patch grid Rohit Modee (Wed Aug 15 2018 - 04:34:52 CDT)
Fwd: Sudden /\A drop in last FEP window Francesco Pietra (Tue Aug 14 2018 - 23:44:06 CDT)
AW: Periodic cell has become too small for original patch grid Norman Geist (Tue Aug 14 2018 - 01:28:06 CDT)
Re: Periodic cell has become too small for original patch grid Giacomo Fiorin (Mon Aug 13 2018 - 07:00:35 CDT)
Periodic cell has become too small for original patch grid Rohit Modee (Mon Aug 13 2018 - 03:26:13 CDT)
Research Programmer Positions Available JoÃ£o Ribeiro (Fri Aug 10 2018 - 13:29:41 CDT)
Re: restarting Gaussian accelerated MD fails David Hardy (Wed Aug 08 2018 - 11:35:44 CDT)
Re: accelMDdihe is not working properly in NAMD after commit e3e849639982dcba9a60c6072c81fdb7cba69759 David Hardy (Wed Aug 08 2018 - 11:26:50 CDT)
How to make water stay in the Z direction? Yi Lun Lee (Wed Aug 08 2018 - 11:26:11 CDT)
Re: accelMDbdihe is not working properly in NAMD after commit e3e849639982dcba9a60c6072c81fdb7cba69759 Omid Bavi (Tue Aug 07 2018 - 13:49:39 CDT)
Re: accelMDdihe is not working properly in NAMD after commit e3e849639982dcba9a60c6072c81fdb7cba69759 Alexander Adams (Tue Aug 07 2018 - 11:43:30 CDT)
atom moving fast error in Coarse grained simulation: even reduced the time step Rabeta Yeasmin (Mon Aug 06 2018 - 14:30:40 CDT)
Re: Sudden /\A drop in last FEP window Francesco Pietra (Mon Aug 06 2018 - 09:30:28 CDT)
question when apply external electric field Jiali Wang (Sat Aug 04 2018 - 16:43:04 CDT)
Re: ParseFEP error with FEP in segments at different lambda schedule Francesco Pietra (Sat Aug 04 2018 - 08:21:10 CDT)
Re: restarting Gaussian accelerated MD fails Miao, Yinglong (Fri Aug 03 2018 - 16:58:34 CDT)
RE: Which one is more reliable to use in umbrella sampling- .traj data or vmd script data Vermaas, Joshua (Fri Aug 03 2018 - 13:55:43 CDT)
Re: Which one is more reliable to use in umbrella sampling- .traj data or vmd script data Giacomo Fiorin (Fri Aug 03 2018 - 13:03:11 CDT)
convert a 3d system into a 2d system Yi Lun Lee (Fri Aug 03 2018 - 11:51:03 CDT)
Re: Which one is more reliable to use in umbrella sampling- .traj data or vmd script data Rabeta Yeasmin (Fri Aug 03 2018 - 10:41:28 CDT)
restarting Gaussian accelerated MD fails Vlad Cojocaru (Fri Aug 03 2018 - 07:00:30 CDT)
Vibration Analysis Script Aashish Bhatt (Fri Aug 03 2018 - 05:16:24 CDT)
Re: Which one is more reliable to use in umbrella sampling- .traj data or vmd script data Giacomo Fiorin (Thu Aug 02 2018 - 22:33:16 CDT)
Which one is more reliable to use in umbrella sampling- .traj data or vmd script data Rabeta Yeasmin (Thu Aug 02 2018 - 16:24:35 CDT)
Re: Rattle error with lateral pressure calculations Sadegh Faramarzi Ganjabad (Thu Aug 02 2018 - 13:28:52 CDT)
Re: Problems with temperature control. Josep Ivan Balaguer Molins (Wed Aug 01 2018 - 12:34:30 CDT)
Re: ParseFEP error with FEP in segments at different lambda schedule Francesco Pietra (Wed Aug 01 2018 - 09:10:54 CDT)
SegFault in QM/MM run Gerard Rowe (Wed Aug 01 2018 - 08:59:37 CDT)
Re: ParseFEP error with FEP in segments at different lambda schedule Brian Radak (Wed Aug 01 2018 - 06:53:18 CDT)
Re: Isomerization between runs Ajasja LjubetiÄ (Wed Aug 01 2018 - 06:40:19 CDT)
RE: Isomerization between runs Vermaas, Joshua (Wed Aug 01 2018 - 06:10:27 CDT)
Re: ParseFEP error with FEP in segments at different lambda schedule Francesco Pietra (Wed Aug 01 2018 - 05:40:22 CDT)
Isomerization between runs Michail Lazaratos (Wed Aug 01 2018 - 04:56:01 CDT)
Re: Problems with temperature control. Brian Radak (Tue Jul 31 2018 - 14:57:09 CDT)
RE: Problems with temperature control. Vermaas, Joshua (Tue Jul 31 2018 - 14:18:35 CDT)
Re: Problems with temperature control. Brian Radak (Tue Jul 31 2018 - 12:57:43 CDT)
Re: Rattle error with lateral pressure calculations Brian Radak (Tue Jul 31 2018 - 12:41:31 CDT)
Re: Problems with temperature control. Josep Ivan Balaguer Molins (Tue Jul 31 2018 - 10:54:40 CDT)
Re: Problems with temperature control. Brian Radak (Tue Jul 31 2018 - 06:56:59 CDT)
Re: Problems with temperature control. Josep Ivan Balaguer Molins (Tue Jul 31 2018 - 06:37:49 CDT)
Re: Problems with temperature control. Josep Ivan Balaguer Molins (Tue Jul 31 2018 - 01:24:58 CDT)
Re: 1-D ABF and Compressibility McGuire, Kelly (Mon Jul 30 2018 - 17:14:49 CDT)
"Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL, September 10-14, 2018 JoÃ£o Ribeiro (Mon Jul 30 2018 - 16:15:45 CDT)
1-D ABF and Compressibility McGuire, Kelly (Mon Jul 30 2018 - 14:44:53 CDT)
Re: Problems with temperature control. Brian Radak (Mon Jul 30 2018 - 13:31:20 CDT)
Re: Problems with temperature control. Josep Ivan Balaguer Molins (Mon Jul 30 2018 - 09:41:32 CDT)
Re: Reg autioionize plugin JoÃ£o Ribeiro (Mon Jul 30 2018 - 09:09:24 CDT)
Re: Problems with temperature control. Brian Radak (Mon Jul 30 2018 - 08:41:29 CDT)
Re: Rattle error with lateral pressure calculations Brian Radak (Mon Jul 30 2018 - 08:29:44 CDT)
Problems with temperature control. Josep Ivan Balaguer Molins (Mon Jul 30 2018 - 05:21:09 CDT)
Re: Rattle error with lateral pressure calculations Sadegh Faramarzi Ganjabad (Sun Jul 29 2018 - 22:18:39 CDT)
Re: Rattle error with lateral pressure calculations Brian Radak (Sat Jul 28 2018 - 12:17:53 CDT)
Re: Multi-dimensional PMF JC Gumbart (Sat Jul 28 2018 - 09:48:08 CDT)
Fwd: Sudden /\A drop in last FEP window Francesco Pietra (Sat Jul 28 2018 - 05:30:07 CDT)
Reg autioionize plugin Vidhya Sankar (Sat Jul 28 2018 - 01:19:09 CDT)
Re: Multi-dimensional PMF McGuire, Kelly (Fri Jul 27 2018 - 23:25:11 CDT)
Re: Multi-dimensional PMF Giacomo Fiorin (Fri Jul 27 2018 - 22:49:55 CDT)
Re: Multi-dimensional PMF Jeff Comer (Fri Jul 27 2018 - 18:39:37 CDT)
RE: Multi-dimensional PMF Vermaas, Joshua (Fri Jul 27 2018 - 14:43:26 CDT)
Re: Multi-dimensional PMF McGuire, Kelly (Fri Jul 27 2018 - 13:07:51 CDT)
Re: Multi-dimensional PMF McGuire, Kelly (Fri Jul 27 2018 - 12:04:34 CDT)
RE: Multi-dimensional PMF Vermaas, Joshua (Fri Jul 27 2018 - 11:27:45 CDT)
Re: Multi-dimensional PMF McGuire, Kelly (Fri Jul 27 2018 - 10:38:58 CDT)
Re: Multi-dimensional PMF McGuire, Kelly (Fri Jul 27 2018 - 09:58:43 CDT)
Re: mail about autoionize plugin JoÃ£o Ribeiro (Fri Jul 27 2018 - 08:07:33 CDT)
Fwd: Sudden /\A drop in last FEP window Francesco Pietra (Fri Jul 27 2018 - 03:13:46 CDT)
Re: [NAMD] Define time-dependent grid force The Cromicus Productions (Thu Jul 26 2018 - 18:57:14 CDT)
Multi-dimensional PMF McGuire, Kelly (Thu Jul 26 2018 - 16:40:28 CDT)
Re: Re: QM/MM with Orca: Memory allocation failed David Hardy (Thu Jul 26 2018 - 14:33:03 CDT)
Re: Sudden /\A drop in last FEP window Francesco Pietra (Thu Jul 26 2018 - 12:54:12 CDT)
Sudden /\A drop in last FEP window Francesco Pietra (Thu Jul 26 2018 - 10:34:06 CDT)
mail about autoionize plugin Vidhya Sankar (Thu Jul 26 2018 - 08:34:43 CDT)
Re: Re: Multiple Colvars Giacomo Fiorin (Wed Jul 25 2018 - 18:03:21 CDT)
Re: Multiple Colvars McGuire, Kelly (Wed Jul 25 2018 - 10:26:46 CDT)
Re: Multiple Colvars McGuire, Kelly (Wed Jul 25 2018 - 09:32:31 CDT)
Re: Multiple Colvars Giacomo Fiorin (Tue Jul 24 2018 - 22:28:57 CDT)
Re: overlapping windows in ABF Giacomo Fiorin (Tue Jul 24 2018 - 22:24:52 CDT)
reg nan error in namd Vidhya Sankar (Tue Jul 24 2018 - 21:00:50 CDT)
Re: overlapping windows in ABF Olya Kravchenko (Tue Jul 24 2018 - 18:37:44 CDT)
Rattle error with lateral pressure calculations Sadegh Faramarzi Ganjabad (Tue Jul 24 2018 - 17:24:17 CDT)
RE: Multiple Colvars Vermaas, Joshua (Tue Jul 24 2018 - 16:59:23 CDT)
Re: Re: QM/MM with Orca: Memory allocation failed Marcelo C. R. Melo (Tue Jul 24 2018 - 16:28:01 CDT)
Multiple Colvars McGuire, Kelly (Tue Jul 24 2018 - 15:38:22 CDT)
REMD restart tcl script meaning? Jacob Usadi (Tue Jul 24 2018 - 12:51:06 CDT)
Re: QM/MM with Orca: Memory allocation failed Gerard Rowe (Tue Jul 24 2018 - 10:55:53 CDT)
RE: Umbrella Sampling input parameters Vermaas, Joshua (Tue Jul 24 2018 - 09:45:08 CDT)
MAIL about namd velocity error Vidhya Sankar (Tue Jul 24 2018 - 09:08:08 CDT)
Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately? Nassar, Omneya (Tue Jul 24 2018 - 07:29:13 CDT)
Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately? JÃ©rÃ´me HÃ©nin (Tue Jul 24 2018 - 02:55:40 CDT)
velocity.pdb and velocity unit in NAMD Kowsar Khajeh (Tue Jul 24 2018 - 01:07:13 CDT)
Re: Umbrella Sampling input parameters Junwoong Yoon (Mon Jul 23 2018 - 23:18:58 CDT)
Re: Abhijit Gogoi (Mon Jul 23 2018 - 22:54:06 CDT)
Re: Giacomo Fiorin (Mon Jul 23 2018 - 17:09:14 CDT)
Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately? JÃ©rÃ´me HÃ©nin (Mon Jul 23 2018 - 16:12:28 CDT)
overlapping windows in ABF Olya Kravchenko (Mon Jul 23 2018 - 09:52:39 CDT)
Re: ABF Questions Giacomo Fiorin (Mon Jul 23 2018 - 08:27:06 CDT)
Re: ABF Questions McGuire, Kelly (Sat Jul 21 2018 - 14:06:51 CDT)
Re: ABF Questions Giacomo Fiorin (Sat Jul 21 2018 - 13:44:52 CDT)
Re: ABF Questions McGuire, Kelly (Sat Jul 21 2018 - 09:52:31 CDT)
Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately? Nassar, Omneya (Sat Jul 21 2018 - 07:58:40 CDT)
Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately? JÃ©rÃ´me HÃ©nin (Sat Jul 21 2018 - 05:58:02 CDT)
Re: [NAMD] Define time-dependent grid force Giacomo Fiorin (Fri Jul 20 2018 - 21:29:25 CDT)
Re: ABF Questions McGuire, Kelly (Fri Jul 20 2018 - 21:20:25 CDT)
ABF Questions McGuire, Kelly (Fri Jul 20 2018 - 21:13:43 CDT)
Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately? Nassar, Omneya (Fri Jul 20 2018 - 15:04:17 CDT)
[NAMD] Define time-dependent grid force The Cromicus Productions (Fri Jul 20 2018 - 12:52:13 CDT)
Re: E-filed to individual channel in parallel system - Reg The Cromicus Productions (Fri Jul 20 2018 - 12:48:21 CDT)
RE: Question about the fundamentals of MD and WHAM Vermaas, Joshua (Fri Jul 20 2018 - 11:35:19 CDT)
Re: Question about the fundamentals of MD and WHAM Giacomo Fiorin (Fri Jul 20 2018 - 07:42:40 CDT)
(no subject) Abhijit Gogoi (Fri Jul 20 2018 - 01:15:37 CDT)
Re: Is QM/MM compatible with Colvars? Giacomo Fiorin (Thu Jul 19 2018 - 16:24:07 CDT)
Fwd: Is QM/MM compatible with Colvars? William Tao (Thu Jul 19 2018 - 16:20:43 CDT)
Is QM/MM compatible with Colvars? William Tao (Thu Jul 19 2018 - 16:16:35 CDT)
RE: Umbrella Sampling input parameters Vermaas, Joshua (Thu Jul 19 2018 - 15:53:25 CDT)
Question about the fundamentals of MD and WHAM Junwoong Yoon (Thu Jul 19 2018 - 15:52:43 CDT)
Re: QM/MM with Orca: Memory allocation failed Marcelo C. R. Melo (Thu Jul 19 2018 - 09:51:25 CDT)
QM/MM with Orca: Memory allocation failed Gerard Rowe (Wed Jul 18 2018 - 17:18:33 CDT)
Re: CHARMM FF parameters for FE-S bond in CYP450 jeevan gc (Wed Jul 18 2018 - 11:20:37 CDT)
RE: NAMD Error Vermaas, Joshua (Wed Jul 18 2018 - 07:45:36 CDT)
Re: CHARMM FF parameters for FE-S bond in CYP450 jeevan gc (Tue Jul 17 2018 - 18:43:50 CDT)
Re: CHARMM FF parameters for FE-S bond in CYP450 JC Gumbart (Tue Jul 17 2018 - 16:54:12 CDT)
CHARMM FF parameters for FE-S bond in CYP450 jeevan gc (Tue Jul 17 2018 - 16:39:50 CDT)
Re: NAMD Error Brian Radak (Tue Jul 17 2018 - 16:32:50 CDT)
Re: NAMD Error Brian Radak (Tue Jul 17 2018 - 15:17:16 CDT)
NAMD Error Shriya Bansal (Tue Jul 17 2018 - 14:45:26 CDT)
E-filed to individual channel in parallel system - Reg Mani Kandan (Tue Jul 17 2018 - 12:09:57 CDT)
Converting GromacsForce File to NAMD using GromacsTopFile.C Ivan (Tue Jul 17 2018 - 06:25:58 CDT)
Re: Consulting about buying new hardware (GPU) michael zhenin (Sun Jul 15 2018 - 06:47:22 CDT)
Re: Decreasing performance of cluster running FEP Francesco Pietra (Sat Jul 14 2018 - 10:57:38 CDT)
Re: Decreasing performance of cluster running FEP Brian Radak (Sat Jul 14 2018 - 09:24:47 CDT)
RE: Umbrella Sampling input parameters Vermaas, Joshua (Fri Jul 13 2018 - 20:30:39 CDT)
Re: Umbrella Sampling input parameters Junwoong Yoon (Thu Jul 12 2018 - 17:45:19 CDT)
Re: Decreasing performance of cluster running FEP Brian Radak (Thu Jul 12 2018 - 09:24:19 CDT)
Re: Decreasing performance of cluster running FEP Francesco Pietra (Thu Jul 12 2018 - 01:58:45 CDT)
RE: Decreasing performance of cluster running FEP Vermaas, Joshua (Wed Jul 11 2018 - 18:23:23 CDT)
RE: Included Topology (.itp) in gromacs to parameter file for NAMD Vermaas, Joshua (Wed Jul 11 2018 - 18:18:44 CDT)
Re: Consulting about buying new hardware (GPU) Lewis J Martin (Wed Jul 11 2018 - 18:13:10 CDT)
Re: Decreasing performance of cluster running FEP Francesco Pietra (Wed Jul 11 2018 - 16:31:55 CDT)
RE: Decreasing performance of cluster running FEP Vermaas, Joshua (Wed Jul 11 2018 - 12:21:07 CDT)
RE: Included Topology (.itp) in gromacs to parameter file for NAMD Vermaas, Joshua (Wed Jul 11 2018 - 12:16:11 CDT)
Decreasing performance of cluster running FEP Francesco Pietra (Wed Jul 11 2018 - 00:29:51 CDT)
Re: ABF Asymmetry McGuire, Kelly (Tue Jul 10 2018 - 12:20:05 CDT)
Re: Broken Structure after reverting coarse-grained system to all-atom system Rabeta Yeasmin (Tue Jul 10 2018 - 09:46:07 CDT)
Re: Consulting about buying new hardware (GPU) JC Gumbart (Tue Jul 10 2018 - 09:45:27 CDT)
Re: Broken Structure after reverting coarse-grained system to all-atom system Peter Freddolino (Tue Jul 10 2018 - 09:07:44 CDT)
Re: ABF Asymmetry Brian Radak (Tue Jul 10 2018 - 07:26:07 CDT)
RE: Umbrella Sampling input parameters Vermaas, Joshua (Tue Jul 10 2018 - 05:40:51 CDT)
Consulting about buying new hardware (GPU) michael zhenin (Tue Jul 10 2018 - 03:44:31 CDT)
Umbrella Sampling input parameters Junwoong Yoon (Tue Jul 10 2018 - 01:55:16 CDT)
Re: ABF Asymmetry McGuire, Kelly (Tue Jul 10 2018 - 00:11:43 CDT)
Re: ABF Asymmetry Brian Radak (Mon Jul 09 2018 - 20:17:02 CDT)
ABF Asymmetry McGuire, Kelly (Mon Jul 09 2018 - 16:48:51 CDT)
Re: ABF simulations with singularities? Junwoong Yoon (Mon Jul 09 2018 - 15:11:48 CDT)
Broken Structure after reverting coarse-grained system to all-atom system Rabeta Yeasmin (Mon Jul 09 2018 - 13:38:42 CDT)
Re: ABF simulations with singularities? Giacomo Fiorin (Mon Jul 09 2018 - 13:00:03 CDT)
Re: ABF simulations with singularities? Junwoong Yoon (Mon Jul 09 2018 - 12:58:31 CDT)
Re: ABF simulations with singularities? Junwoong Yoon (Mon Jul 09 2018 - 12:52:09 CDT)
Re: Qwikmd ABF Question JoÃ£o Ribeiro (Mon Jul 09 2018 - 08:18:48 CDT)
Re: Total charge problem Abhishek Kumar Singh (Sat Jul 07 2018 - 11:42:15 CDT)
Re: Total charge problem Victor Kwan (Fri Jul 06 2018 - 18:50:36 CDT)
Re: ABF, rigid bonds and constraints Ekaterina Sobakinskaja (Fri Jul 06 2018 - 10:06:21 CDT)
ABF, rigid bonds and constraints Ekaterina Sobakinskaja (Fri Jul 06 2018 - 05:23:10 CDT)
ABF simulations with singularities? Junwoong Yoon (Thu Jul 05 2018 - 20:55:29 CDT)
Re: Distorted peptide bond with new residue Brian Radak (Thu Jul 05 2018 - 19:23:06 CDT)
Re: Distorted peptide bond with new residue Nick Palmer (Thu Jul 05 2018 - 17:39:25 CDT)
RE: Distorted peptide bond with new residue Vermaas, Joshua (Thu Jul 05 2018 - 17:05:54 CDT)
Re: Distorted peptide bond with new residue Nick Palmer (Thu Jul 05 2018 - 17:00:25 CDT)
RE: Distorted peptide bond with new residue Vermaas, Joshua (Thu Jul 05 2018 - 16:34:02 CDT)
Distorted peptide bond with new residue Nick Palmer (Thu Jul 05 2018 - 16:18:28 CDT)
RE: Total charge problem Vermaas, Joshua (Thu Jul 05 2018 - 15:22:24 CDT)
Re: Total charge problem Abhishek Kumar Singh (Thu Jul 05 2018 - 13:29:40 CDT)
Re: Qwikmd ABF Question JoÃ£o Ribeiro (Thu Jul 05 2018 - 13:16:01 CDT)
Re: Qwikmd ABF Question McGuire, Kelly (Thu Jul 05 2018 - 10:48:41 CDT)
Re: Qwikmd ABF Question JoÃ£o Ribeiro (Thu Jul 05 2018 - 08:03:31 CDT)
Re: Qwikmd ABF Question McGuire, Kelly (Wed Jul 04 2018 - 19:35:02 CDT)
Re: Qwikmd ABF Question JoÃ£o Ribeiro (Wed Jul 04 2018 - 19:25:30 CDT)
Re: Qwikmd ABF Question McGuire, Kelly (Wed Jul 04 2018 - 18:44:26 CDT)
Bond parameter error for the system which has been converted using residue-based coarse-grained method Rabeta Yeasmin (Wed Jul 04 2018 - 15:25:24 CDT)
Re: Equilibration in NPT simulation Peter Freddolino (Wed Jul 04 2018 - 13:37:31 CDT)
Re: Equilibration in NPT simulation Mani Kandan (Wed Jul 04 2018 - 11:59:38 CDT)
RE: Total charge problem Vermaas, Joshua (Wed Jul 04 2018 - 11:51:09 CDT)
Re: Equilibration in NPT simulation Mani Kandan (Wed Jul 04 2018 - 11:30:50 CDT)
Re: Qwikmd ABF Question McGuire, Kelly (Wed Jul 04 2018 - 11:21:57 CDT)
Re: Qwikmd ABF Question McGuire, Kelly (Wed Jul 04 2018 - 11:21:21 CDT)
Re: Equilibration in NPT simulation Kowsar Khajeh (Wed Jul 04 2018 - 10:46:47 CDT)
Equilibration in NPT simulation Mani Kandan (Wed Jul 04 2018 - 10:25:19 CDT)
Re: NAMD SMP version warning - Reg Mani Kandan (Wed Jul 04 2018 - 09:59:35 CDT)
AW: NAMD SMP version warning - Reg Norman Geist (Wed Jul 04 2018 - 09:42:45 CDT)
Re: Qwikmd ABF Question JoÃ£o Ribeiro (Wed Jul 04 2018 - 08:08:10 CDT)
Total charge problem Abhishek Kumar Singh (Wed Jul 04 2018 - 07:50:36 CDT)
Ph.D. candidate position in biomolecular modeling or bioinformatics Jan Brezovsky (Wed Jul 04 2018 - 05:33:36 CDT)
AW: NAMD SMP version warning - Reg Norman Geist (Wed Jul 04 2018 - 05:18:45 CDT)
AW: NAMD SMP version warning - Reg Norman Geist (Wed Jul 04 2018 - 05:12:46 CDT)
NAMD SMP version warning - Reg Mani Kandan (Wed Jul 04 2018 - 04:57:40 CDT)
Qwikmd ABF Question McGuire, Kelly (Wed Jul 04 2018 - 02:42:39 CDT)
Re: Random Velocities Question McGuire, Kelly (Tue Jul 03 2018 - 22:46:05 CDT)
Re: Random Velocities Question Axel Kohlmeyer (Tue Jul 03 2018 - 22:37:39 CDT)
RE: Random Velocities Question Vermaas, Joshua (Tue Jul 03 2018 - 22:37:39 CDT)
Random Velocities Question McGuire, Kelly (Tue Jul 03 2018 - 22:09:44 CDT)
RE: Included Topology (.itp) in gromacs to parameter file for NAMD Vermaas, Joshua (Tue Jul 03 2018 - 11:51:12 CDT)
Included Topology (.itp) in gromacs to parameter file for NAMD Ivan (Tue Jul 03 2018 - 03:40:29 CDT)
Problem in NAMD memory optimized version - Reg Mani Kandan (Mon Jul 02 2018 - 11:02:37 CDT)
Re: At high cutoff: "ERROR: CALCULATED VDWA FORCE MAY NOT MATCH ENERGY! POSSIBLE BUG!" Brian Radak (Sun Jul 01 2018 - 12:21:03 CDT)
At high cutoff: "ERROR: CALCULATED VDWA FORCE MAY NOT MATCH ENERGY! POSSIBLE BUG!" Victor Kwan (Sat Jun 30 2018 - 15:35:08 CDT)
Re: ABF Question Haohao Fu (Fri Jun 29 2018 - 01:29:23 CDT)
ABF Question McGuire, Kelly (Thu Jun 28 2018 - 23:59:03 CDT)
QMMM FEP SM Bargeen A Turzo (Thu Jun 28 2018 - 14:38:31 CDT)
Re: QwikMD Question JoÃ£o Ribeiro (Thu Jun 28 2018 - 12:08:13 CDT)
QwikMD Question McGuire, Kelly (Thu Jun 28 2018 - 10:34:17 CDT)
Re: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD JoÃ£o Ribeiro (Wed Jun 27 2018 - 09:47:41 CDT)
Re: Phosphorylated Residues Aysima Hacisuleyman (Wed Jun 27 2018 - 05:54:02 CDT)
Phosphorylated Residues Oscar Bastidas (Tue Jun 26 2018 - 23:29:07 CDT)
Re: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD JoÃ£o Ribeiro (Tue Jun 26 2018 - 18:16:11 CDT)
Re: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD JoÃ£o Ribeiro (Tue Jun 26 2018 - 17:53:38 CDT)
Re: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD Hazel, Anthony J (Tue Jun 26 2018 - 17:48:31 CDT)
Re: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD Hazel, Anthony J (Tue Jun 26 2018 - 17:48:08 CDT)
Re: "Child killed: segmentation violation" error when running QM/MM minimization in QwikMD JoÃ£o Ribeiro (Tue Jun 26 2018 - 17:41:48 CDT)
"Child killed: segmentation violation" error when running QM/MM minimization in QwikMD Hazel, Anthony J (Tue Jun 26 2018 - 17:17:28 CDT)
Re: Hydronium parameters Kinkini Jayasundara (Tue Jun 26 2018 - 11:10:31 CDT)
Hydronium parameters Kinkini Jayasundara (Tue Jun 26 2018 - 10:49:03 CDT)
RE: Colvars Restraint Question Vermaas, Joshua (Mon Jun 25 2018 - 12:18:16 CDT)
Re: Colvars Restraint Question McGuire, Kelly (Mon Jun 25 2018 - 12:15:44 CDT)
RE: Colvars Restraint Question Vermaas, Joshua (Mon Jun 25 2018 - 12:01:53 CDT)
Re: Colvars Restraint Question McGuire, Kelly (Sun Jun 24 2018 - 23:20:31 CDT)
mail about usage of water tcl script in membrane Vidhya Sankar (Sat Jun 23 2018 - 08:09:26 CDT)
Re: Strange Bond Behavior Question Ajasja LjubetiÄ (Sat Jun 23 2018 - 04:54:04 CDT)
Re: vmd-l: Re: Strange Bond Behavior Question McGuire, Kelly (Fri Jun 22 2018 - 21:27:04 CDT)
Re: Strange Bond Behavior Question McGuire, Kelly (Fri Jun 22 2018 - 16:52:49 CDT)
Re: Strange Bond Behavior Question McGuire, Kelly (Fri Jun 22 2018 - 16:17:28 CDT)
Re: Strange Bond Behavior Question Brian Radak (Fri Jun 22 2018 - 16:12:30 CDT)
Re: Strange Bond Behavior Question JoÃ£o Ribeiro (Fri Jun 22 2018 - 16:08:07 CDT)
Strange Bond Behavior Question McGuire, Kelly (Fri Jun 22 2018 - 15:42:20 CDT)
Better way to fix the atom -Reg Mani Kandan (Fri Jun 22 2018 - 10:51:57 CDT)
Re: "block" module for NAMD Brian Radak (Fri Jun 22 2018 - 08:22:10 CDT)
Re: namd mpi Brian Radak (Fri Jun 22 2018 - 08:20:16 CDT)
Re: mail reg constraint force Brian Radak (Fri Jun 22 2018 - 08:14:08 CDT)
"block" module for NAMD Tyler Wied (Fri Jun 22 2018 - 07:56:56 CDT)
namd mpi Stefano Guglielmo (Fri Jun 22 2018 - 07:46:27 CDT)
mail reg constraint force Vidhya Sankar (Fri Jun 22 2018 - 07:04:54 CDT)
Re: Colvars Restraint Question McGuire, Kelly (Thu Jun 21 2018 - 16:45:39 CDT)
RE: Colvars Restraint Question Vermaas, Joshua (Thu Jun 21 2018 - 16:02:54 CDT)
Re: Colvars Restraint Question McGuire, Kelly (Thu Jun 21 2018 - 15:46:49 CDT)
RE: Colvars Restraint Question Vermaas, Joshua (Thu Jun 21 2018 - 15:22:10 CDT)
Re: Colvars Restraint Question McGuire, Kelly (Thu Jun 21 2018 - 15:04:41 CDT)
Re: Colvars Restraint Question Brian Radak (Thu Jun 21 2018 - 15:01:39 CDT)
Re: Colvars Restraint Question McGuire, Kelly (Thu Jun 21 2018 - 14:53:17 CDT)
Re: Colvars Restraint Question Brian Radak (Thu Jun 21 2018 - 14:01:23 CDT)
Re: Colvars Restraint Question McGuire, Kelly (Thu Jun 21 2018 - 13:43:18 CDT)
Re: Colvars Restraint Question Bassam Haddad (Thu Jun 21 2018 - 12:33:58 CDT)
Colvars Restraint Question McGuire, Kelly (Thu Jun 21 2018 - 12:01:18 CDT)
Re: merging abf trajectories with different number of colvars Olya Kravchenko (Thu Jun 21 2018 - 11:22:26 CDT)
Re: merging abf trajectories with different number of colvars Souvik Sinha (Thu Jun 21 2018 - 10:05:30 CDT)
Re: merging abf trajectories with different number of colvars Olya Kravchenko (Thu Jun 21 2018 - 09:19:17 CDT)
mail about constraints in namd configuration file Vidhya Sankar (Thu Jun 21 2018 - 07:52:17 CDT)
Re: merging abf trajectories with different number of colvars Olya Kravchenko (Wed Jun 20 2018 - 13:18:11 CDT)
Re: problem with minimizer Victor Kwan (Wed Jun 20 2018 - 11:04:50 CDT)
problem with minimizer Laura Joana (Wed Jun 20 2018 - 07:53:41 CDT)
RE: [NAMD] Apply an electric field only in a specific region Vermaas, Joshua (Tue Jun 19 2018 - 08:41:14 CDT)
Re: [NAMD] Apply an electric field only in a specific region The Cromicus Productions (Tue Jun 19 2018 - 03:41:15 CDT)
Re: PCA and vector Dhiraj Srivastava (Sat Jun 16 2018 - 13:03:57 CDT)
Re: electric field- forces in NAMD source code Kowsar Khajeh (Sat Jun 16 2018 - 06:17:31 CDT)
electric field- forces in NAMD source code Kowsar Khajeh (Sat Jun 16 2018 - 02:25:29 CDT)
PCA and vector Dhiraj Srivastava (Fri Jun 15 2018 - 13:59:07 CDT)
RE: Vermaas, Joshua (Fri Jun 15 2018 - 04:34:48 CDT)
Re: Laura Tiessler (Thu Jun 14 2018 - 13:38:28 CDT)
Re: Error during simulation Victor Kwan (Thu Jun 14 2018 - 12:22:45 CDT)
Re: GaMD in NAMD Miao, Yinglong (Thu Jun 14 2018 - 08:46:45 CDT)
Re: GaMD in NAMD Dhiraj Srivastava (Thu Jun 14 2018 - 07:40:52 CDT)
AW: AW: How to run a TCL proc at every step in NAMD using callback command? Norman Geist (Thu Jun 14 2018 - 04:13:18 CDT)
Re: AW: How to run a TCL proc at every step in NAMD using callback command? yjcoshc (Thu Jun 14 2018 - 04:06:40 CDT)
AW: How to run a TCL proc at every step in NAMD using callback command? Norman Geist (Thu Jun 14 2018 - 03:38:08 CDT)
How to run a TCL proc at every step in NAMD using callback command? yjcoshc (Thu Jun 14 2018 - 03:10:32 CDT)
Re: GaMD in NAMD Francesco Pietra (Thu Jun 14 2018 - 01:05:52 CDT)
Re: GaMD in NAMD Dhiraj Srivastava (Wed Jun 13 2018 - 23:51:07 CDT)
Re: GaMD in NAMD Alexander Adams (Wed Jun 13 2018 - 23:15:12 CDT)
Re: GaMD in NAMD Dhiraj Srivastava (Wed Jun 13 2018 - 22:09:46 CDT)
Re: GaMD in NAMD Chitrak Gupta (Wed Jun 13 2018 - 22:04:51 CDT)
GaMD in NAMD Dhiraj Srivastava (Wed Jun 13 2018 - 21:54:19 CDT)
Re: non uniform attempts distribution in constant pH MD Brian Radak (Wed Jun 13 2018 - 10:27:59 CDT)
Error during simulation shyam sharma (Wed Jun 13 2018 - 06:27:46 CDT)
non uniform attempts distribution in constant pH MD Yasser Bruno Ruiz Blanco (Wed Jun 13 2018 - 06:04:10 CDT)
RE: mail about non bonded parameters Vermaas, Joshua (Wed Jun 13 2018 - 05:13:09 CDT)
Re: nonuniform sampling in ABF Haohao Fu (Tue Jun 12 2018 - 11:25:39 CDT)
nonuniform sampling in ABF Artur Hermano (Tue Jun 12 2018 - 10:28:28 CDT)
mail about non bonded parameters Vidhya Sankar (Mon Jun 11 2018 - 20:58:09 CDT)
Re: PMF calculation using CPU and GPU Souvik Sinha (Fri Jun 08 2018 - 10:04:51 CDT)
RE: psf from parmed Vermaas, Joshua (Fri Jun 08 2018 - 09:30:11 CDT)
Re: psf from parmed Stefano Guglielmo (Fri Jun 08 2018 - 09:20:59 CDT)
RE: psf from parmed Vermaas, Joshua (Fri Jun 08 2018 - 09:03:43 CDT)
Re: PMF calculation using CPU and GPU Giacomo Fiorin (Fri Jun 08 2018 - 08:55:15 CDT)
PMF calculation using CPU and GPU Souvik Sinha (Fri Jun 08 2018 - 08:36:27 CDT)
psf from parmed Stefano Guglielmo (Fri Jun 08 2018 - 08:09:16 CDT)
Mail about force field parameters Vidhya Sankar (Thu Jun 07 2018 - 21:25:38 CDT)
Re: David Hardy (Thu Jun 07 2018 - 14:18:06 CDT)
Requesting abstracts for MRS Fall 2018 Symposium BM03: Multiscale Modeling of Soft Materials and Interfaces Sanket Deshmukh (Thu Jun 07 2018 - 09:22:42 CDT)
Re: AMBER NetCDF file for Simulation Brian Radak (Thu Jun 07 2018 - 09:18:39 CDT)
(no subject) Laura Tiessler (Thu Jun 07 2018 - 06:24:00 CDT)
Re: AMBER NetCDF file for Simulation Aashish Bhatt (Thu Jun 07 2018 - 02:02:31 CDT)
BUG: ReplicaUniformPatchGrids and "output" command namd-2.13NB Norman Geist (Thu Jun 07 2018 - 01:56:47 CDT)
Re: AMBER NetCDF file for Simulation Brian Radak (Wed Jun 06 2018 - 09:12:17 CDT)
AMBER NetCDF file for Simulation Aashish Bhatt (Wed Jun 06 2018 - 07:33:10 CDT)
Sudden drop of /\A in ParseFEP.log near lamda 1.0 Francesco Pietra (Wed Jun 06 2018 - 00:58:11 CDT)
Re: enhanced sampling of flexible tail Brian Radak (Tue Jun 05 2018 - 16:16:15 CDT)
enhanced sampling of flexible tail Dhiraj Srivastava (Tue Jun 05 2018 - 16:02:08 CDT)
Re: namd2_ti.pl Error: Modification of non-creatable array value attempted Brian Radak (Mon Jun 04 2018 - 08:14:11 CDT)
Re: NAMD+PLUMED Giacomo Fiorin (Mon Jun 04 2018 - 06:48:05 CDT)
Re: [NAMD] Apply an electric field only in a specific region Giacomo Fiorin (Mon Jun 04 2018 - 06:33:27 CDT)
Re: [NAMD] Apply an electric field only in a specific region Kowsar Khajeh (Mon Jun 04 2018 - 02:46:12 CDT)
[NAMD] Apply an electric field only in a specific region The Cromicus Productions (Mon Jun 04 2018 - 01:39:28 CDT)
namd2_ti.pl Error: Modification of non-creatable array value attempted Kooshul S. Jhaveri (Sun Jun 03 2018 - 11:34:09 CDT)
Update particle position iteratively in between steps Nate Walkins (Sun Jun 03 2018 - 09:55:29 CDT)
Re: NAMD+PLUMED jing liang (Sun Jun 03 2018 - 05:15:09 CDT)
RE: NAMD+PLUMED Vermaas, Joshua (Sat Jun 02 2018 - 22:03:22 CDT)
Re: NAMD+PLUMED Giacomo Fiorin (Sat Jun 02 2018 - 16:25:26 CDT)
NAMD+PLUMED jing liang (Sat Jun 02 2018 - 13:34:26 CDT)
RE: mail about error in namd compilation Vermaas, Joshua (Fri Jun 01 2018 - 11:05:15 CDT)
mail about error in namd compilation Vidhya Sankar (Fri Jun 01 2018 - 03:08:09 CDT)
Re: temperature accelerated molecular dynamics yjcoshc (Fri Jun 01 2018 - 01:54:18 CDT)
temperature accelerated molecular dynamics Dhiraj Srivastava (Thu May 31 2018 - 23:59:35 CDT)
MAIL REG NAMD PBS SCRIPT on mpi cluster Vidhya Sankar (Thu May 31 2018 - 23:15:09 CDT)
Re: Issue using qwikMD with an uncommon cofactor Marcelo C. R. Melo (Thu May 31 2018 - 17:55:02 CDT)
merging abf trajectories with different number of colvars Olya Kravchenko (Thu May 31 2018 - 11:13:50 CDT)
Re: Problem in generating psf Peter Freddolino (Thu May 31 2018 - 07:31:46 CDT)
Problem in generating psf Srijita Paul (Thu May 31 2018 - 01:25:39 CDT)
Microtubule Simulation Alex Saad-Falcon (Wed May 30 2018 - 17:13:40 CDT)
Re: "non-numeric floating-point value" error while using distanceXY Olya Kravchenko (Wed May 30 2018 - 11:40:18 CDT)
"non-numeric floating-point value" error while using distanceXY Olya Kravchenko (Wed May 30 2018 - 09:06:00 CDT)
Mail from vidhyasankar Vidhya Sankar (Tue May 29 2018 - 22:10:49 CDT)
Re: Difference between REMD replica temperature and actual temperature jozs2019_at_uni.sydney.edu.au (Tue May 29 2018 - 18:19:31 CDT)
Re: Re: vmd-l: Large number of harmonic distance restraints Giacomo Fiorin (Tue May 29 2018 - 12:53:52 CDT)
Re: Re: vmd-l: Large number of harmonic distance restraints Brian Radak (Tue May 29 2018 - 12:37:00 CDT)
Re: mail reg Namd compilation David Hardy (Tue May 29 2018 - 11:38:42 CDT)
Re: Re: vmd-l: Large number of harmonic distance restraints Ajasja LjubetiÄ (Tue May 29 2018 - 11:36:46 CDT)
Re: vmd-l: Large number of harmonic distance restraints Axel Kohlmeyer (Tue May 29 2018 - 11:26:36 CDT)
Re: Solutescaling not working with Amber files Brian Radak (Tue May 29 2018 - 09:47:15 CDT)
Solutescaling not working with Amber files Norman Geist (Tue May 29 2018 - 06:06:57 CDT)
Info on solutescaling Norman Geist (Tue May 29 2018 - 02:13:27 CDT)
AW: Difference between REMD replica temperature and actual temperature Norman Geist (Tue May 29 2018 - 02:12:11 CDT)
AW: Difference between REMD replica temperature and actual temperature Norman Geist (Tue May 29 2018 - 02:08:12 CDT)
Difference between REMD replica temperature and actual temperature jozs2019_at_uni.sydney.edu.au (Mon May 28 2018 - 21:03:05 CDT)
Re: Periodic cell basis too small for GridForce Ryan McGreevy (Mon May 28 2018 - 11:42:01 CDT)
FEP performance Francesco Pietra (Mon May 28 2018 - 10:05:01 CDT)
Re: mail reg Namd compilation Fotis Baltoumas (Mon May 28 2018 - 04:14:34 CDT)
Re: mail reg Namd compilation Ajasja LjubetiÄ (Mon May 28 2018 - 03:58:48 CDT)
mail reg Namd compilation Vidhya Sankar (Mon May 28 2018 - 03:06:06 CDT)
Periodic cell basis too small for GridForce Carla Gómez Santiago (Sun May 27 2018 - 09:29:30 CDT)
Which parameters to use in the MD simulation of defected carbon nanotube/graphene? jashnvareh 1395 (Sun May 27 2018 - 03:10:25 CDT)
Re: xMDFF: model file is not given Ryan McGreevy (Fri May 25 2018 - 10:31:56 CDT)
xMDFF: model file is not given Antonio Vila Sanjurjo (Fri May 25 2018 - 07:00:32 CDT)
Spectre/Meltdown patch performance hits Bryan Roessler (Thu May 24 2018 - 09:34:00 CDT)
RE: run different simulation of the same system by using different initial velocities Vermaas, Joshua (Thu May 24 2018 - 08:28:06 CDT)
Re: run different simulation of the same system by using different initial velocities Giacomo Fiorin (Thu May 24 2018 - 08:22:46 CDT)
run different simulation of the same system by using different initial velocities Serena Vittorio (Thu May 24 2018 - 07:35:39 CDT)
Re: Segmentation fault Sonibare, Kolawole (Wed May 23 2018 - 16:49:04 CDT)
Segmentation fault Sonibare, Kolawole (Wed May 23 2018 - 13:41:03 CDT)
PBC and restraints Carla Gómez Santiago (Wed May 23 2018 - 11:05:06 CDT)
Re: Creating an infinite graphene sheet jashnvareh 1395 (Sat May 19 2018 - 20:23:17 CDT)
Re: restrain lateral movement during ABF Olya Kravchenko (Fri May 18 2018 - 08:37:24 CDT)
Re: restrain lateral movement during ABF Giacomo Fiorin (Thu May 17 2018 - 17:06:02 CDT)
Re: restrain lateral movement during ABF Olya Kravchenko (Thu May 17 2018 - 16:47:13 CDT)
Re: accelMDdihe is not working properly in NAMD after commit e3e849639982dcba9a60c6072c81fdb7cba69759 David Hardy (Thu May 17 2018 - 10:46:00 CDT)
AW: Are there plans on thermostat groups? Norman Geist (Thu May 17 2018 - 02:25:49 CDT)
restrain lateral movement during ABF Olya Kravchenko (Wed May 16 2018 - 16:34:48 CDT)
Re: Are there plans on thermostat groups? Brian Radak (Wed May 16 2018 - 12:52:09 CDT)
RE: Are there plans on thermostat groups? Vermaas, Joshua (Wed May 16 2018 - 11:33:10 CDT)
Re: Are there plans on thermostat groups? Brian Radak (Wed May 16 2018 - 10:24:00 CDT)
Are there plans on thermostat groups? Norman Geist (Wed May 16 2018 - 09:56:01 CDT)
RE: Creating an infinite graphene sheet Vermaas, Joshua (Wed May 16 2018 - 08:30:50 CDT)
Re: How to create multiple molecules using psfgen Giacomo Fiorin (Wed May 16 2018 - 07:06:12 CDT)
Re: Creating an infinite graphene sheet jashnvareh 1395 (Wed May 16 2018 - 00:54:03 CDT)
accelMDdihe is not working properly in NAMD after commit e3e849639982dcba9a60c6072c81fdb7cba69759 yjcoshc (Tue May 15 2018 - 20:59:09 CDT)
RE: How to create multiple molecules using psfgen Vermaas, Joshua (Tue May 15 2018 - 19:47:10 CDT)
RE: How to create multiple molecules using psfgen Vermaas, Joshua (Tue May 15 2018 - 18:18:25 CDT)
How to create multiple molecules using psfgen Sonibare, Kolawole (Tue May 15 2018 - 17:32:32 CDT)
RE: RE: Hard wall on Z direction for ions Vermaas, Joshua (Tue May 15 2018 - 08:36:16 CDT)
Re: RE: Hard wall on Z direction for ions Fateme Ghadirian (Tue May 15 2018 - 03:28:02 CDT)
NAMD hangs at "Load balancer assumes all CPUs are same." when runs on an infiniband cluster. yjcoshc (Mon May 14 2018 - 22:08:46 CDT)
Re: dummyAtom in distance colvar in ABF calculations Giacomo Fiorin (Mon May 14 2018 - 18:49:02 CDT)
Re: FEP slowdown during execution Brian Radak (Mon May 14 2018 - 15:14:01 CDT)
Re: dummyAtom in distance colvar in ABF calculations Olya Kravchenko (Mon May 14 2018 - 12:37:20 CDT)
Re: Problem generating pdb psf of ATP Brian Radak (Mon May 14 2018 - 11:35:17 CDT)
RE: Hard wall on Z direction for ions Vermaas, Joshua (Mon May 14 2018 - 10:57:10 CDT)
Re: dummyAtom in distance colvar in ABF calculations Olya Kravchenko (Mon May 14 2018 - 10:26:55 CDT)
Hard wall on Z direction for ions Fateme Ghadirian (Mon May 14 2018 - 09:06:31 CDT)
RE: reverting atoms introduced by name into standard PDB ones Vermaas, Joshua (Mon May 14 2018 - 07:55:45 CDT)
Re: reverting atoms introduced by name into standard PDB ones Oleksiy Kovtun (Mon May 14 2018 - 07:44:15 CDT)
RE: reverting atoms introduced by name into standard PDB ones Vermaas, Joshua (Mon May 14 2018 - 07:31:44 CDT)
Re: Problem generating pdb psf of ATP Denish Poudyal (Mon May 14 2018 - 04:55:05 CDT)
reverting atoms introduced by name into standard PDB ones Oleksiy Kovtun (Mon May 14 2018 - 04:45:43 CDT)
Problem generating pdb psf of ATP Srijita Paul (Mon May 14 2018 - 02:33:43 CDT)
RE: Creating an infinite graphene sheet Vermaas, Joshua (Sun May 13 2018 - 13:58:05 CDT)
Re: Creating an infinite graphene sheet Aksimentiev, Aleksei (Sun May 13 2018 - 12:38:52 CDT)
Re: Creating an infinite graphene sheet jashnvareh 1395 (Sun May 13 2018 - 11:23:54 CDT)
Re: Creating an infinite graphene sheet Giacomo Fiorin (Sun May 13 2018 - 10:53:39 CDT)
Re: Creating an infinite graphene sheet jashnvareh 1395 (Sun May 13 2018 - 10:34:11 CDT)
Re: dummyAtom in distance colvar in ABF calculations Giacomo Fiorin (Sun May 13 2018 - 10:16:35 CDT)
Re: Creating an infinite graphene sheet Giacomo Fiorin (Sun May 13 2018 - 10:08:46 CDT)
Re: Creating an infinite graphene sheet jashnvareh 1395 (Sun May 13 2018 - 02:27:42 CDT)
Re: Creating an infinite graphene sheet jashnvareh 1395 (Sun May 13 2018 - 02:13:13 CDT)
Re: Creating an infinite graphene sheet jashnvareh 1395 (Sun May 13 2018 - 02:11:07 CDT)
dummyAtom in distance colvar in ABF calculations Olya Kravchenko (Sat May 12 2018 - 16:44:16 CDT)
RE: Creating an infinite graphene sheet Vermaas, Joshua (Sat May 12 2018 - 16:27:42 CDT)
Re: Creating an infinite graphene sheet Giacomo Fiorin (Sat May 12 2018 - 13:19:11 CDT)
Creating an infinite graphene sheet jashnvareh 1395 (Sat May 12 2018 - 10:34:09 CDT)
Fwd: FEP slowdown during execution Francesco Pietra (Sat May 12 2018 - 01:12:35 CDT)
FEP slowdown during execution Francesco Pietra (Sat May 12 2018 - 01:10:39 CDT)
Re: unit dipole moment vector The Cromicus Productions (Fri May 11 2018 - 13:11:13 CDT)
unit dipole moment vector Suresh Ghimire (Fri May 11 2018 - 02:58:09 CDT)
Re: Get NAMD version from the tcl script interface yjcoshc (Wed May 09 2018 - 19:51:23 CDT)
Re: Get NAMD version from the tcl script interface Ajasja LjubetiÄ (Wed May 09 2018 - 10:43:11 CDT)
Re: Get NAMD version from the tcl script interface Brian Radak (Wed May 09 2018 - 10:38:36 CDT)
Re: Get NAMD version from the tcl script interface Ajasja LjubetiÄ (Wed May 09 2018 - 10:06:48 CDT)
Re: Get NAMD version from the tcl script interface Brian Radak (Wed May 09 2018 - 09:36:44 CDT)
Re: Get NAMD version from the tcl script interface Giacomo Fiorin (Wed May 09 2018 - 06:50:57 CDT)
Get NAMD version from the tcl script interface yjcoshc (Wed May 09 2018 - 03:36:18 CDT)
Re: distance filter during data analysis Souvik Sinha (Wed May 09 2018 - 00:53:43 CDT)
distance filter during data analysis Dhiraj Srivastava (Tue May 08 2018 - 23:43:39 CDT)
Re: Angle of lone pair in TIP4P 2005 simulation Peter Freddolino (Tue May 08 2018 - 23:06:55 CDT)
Re: Angle of lone pair in TIP4P 2005 simulation Monika Madhavi (Tue May 08 2018 - 22:17:16 CDT)
Re: Angle of lone pair in TIP4P 2005 simulation Peter Freddolino (Tue May 08 2018 - 20:37:19 CDT)
RE: Angle of lone pair in TIP4P 2005 simulation Vermaas, Joshua (Tue May 08 2018 - 19:57:31 CDT)
Re: Angle of lone pair in TIP4P 2005 simulation Esmael Jafari Haddadian (Tue May 08 2018 - 19:18:23 CDT)
Angle of lone pair in TIP4P 2005 simulation Geo Reuter (Tue May 08 2018 - 19:08:34 CDT)
Fwd: FEP & node/core number Francesco Pietra (Mon May 07 2018 - 09:34:14 CDT)
Re: FEP & node/core number Brian Radak (Mon May 07 2018 - 08:38:37 CDT)
Re: Missing cphrst file Brian Radak (Mon May 07 2018 - 08:36:38 CDT)
Fwd: FEP & node/core number Francesco Pietra (Mon May 07 2018 - 08:19:22 CDT)
Re: Fwd: FEP protein-ligand tutorial 2017 unclear section Francesco Pietra (Mon May 07 2018 - 08:03:34 CDT)
Missing cphrst file Yasser Bruno Ruiz Blanco (Mon May 07 2018 - 07:59:15 CDT)
Re: Martini CG parameter errors for lipids Hyun (Sun May 06 2018 - 08:52:44 CDT)
Re: Fwd: FEP protein-ligand tutorial 2017 unclear section Chris Chipot (Sat May 05 2018 - 09:28:27 CDT)
Re: Fwd: FEP protein-ligand tutorial 2017 unclear section JC Gumbart (Sat May 05 2018 - 07:20:13 CDT)
Re: Fwd: FEP protein-ligand tutorial 2017 unclear section Francesco Pietra (Sat May 05 2018 - 01:43:17 CDT)
Re: Re: vmd-l: Fwd: FEP with intermediary segments Francesco Pietra (Sat May 05 2018 - 01:21:23 CDT)
Re: Fwd: FEP protein-ligand tutorial 2017 unclear section Giacomo Fiorin (Fri May 04 2018 - 17:04:28 CDT)
Re: Re: vmd-l: Fwd: FEP with intermediary segments Brian Radak (Fri May 04 2018 - 15:46:56 CDT)
Re: Re: vmd-l: Fwd: FEP with intermediary segments Francesco Pietra (Fri May 04 2018 - 15:00:22 CDT)
Re: Fwd: FEP protein-ligand tutorial 2017 unclear section Francesco Pietra (Fri May 04 2018 - 14:47:42 CDT)
Re: AW: Aromatic rings don't maintain the planarity during the heating Serena Vittorio (Fri May 04 2018 - 11:51:39 CDT)
AW: Aromatic rings don't maintain the planarity during the heating Daniel MÃ¶ller (Fri May 04 2018 - 11:23:24 CDT)
Re: How to solve the segmentation faults in compiling NAMD to build and test the Charm++/Converse library (MPI version)? Scott Brozell (Fri May 04 2018 - 11:17:32 CDT)
Aromatic rings don't maintain the planarity during the heating Serena Vittorio (Fri May 04 2018 - 11:14:30 CDT)
Re: Re: vmd-l: Fwd: FEP with intermediary segments Brian Radak (Fri May 04 2018 - 11:04:10 CDT)
Re: Continuing metadynamics run Giacomo Fiorin (Fri May 04 2018 - 10:59:30 CDT)
Re: Re: vmd-l: Fwd: FEP with intermediary segments Francesco Pietra (Fri May 04 2018 - 10:51:45 CDT)
Re: Fwd: FEP protein-ligand tutorial 2017 unclear section JC Gumbart (Fri May 04 2018 - 10:43:47 CDT)
Continuing metadynamics run Rabeta Yeasmin (Fri May 04 2018 - 10:25:08 CDT)
Re: How to solve the segmentation faults in compiling NAMD to build and test the Charm++/Converse library (MPI version)? Brian Radak (Fri May 04 2018 - 08:05:21 CDT)
Re: vmd-l: Fwd: FEP with intermediary segments Brian Radak (Fri May 04 2018 - 08:01:28 CDT)
How to solve the segmentation faults in compiling NAMD to build and test the Charm++/Converse library (MPI version)? LIAO Mingling (Fri May 04 2018 - 07:07:13 CDT)
Fwd: FEP protein-ligand tutorial 2017 unclear section Francesco Pietra (Fri May 04 2018 - 00:39:24 CDT)
Fwd: FEP with intermediary segments Francesco Pietra (Fri May 04 2018 - 00:37:18 CDT)
Re: Brian Radak (Thu May 03 2018 - 08:40:03 CDT)
SM Bargeen A Turzo wants to share the file Min_error with you SM Bargeen A Turzo (Wed May 02 2018 - 21:43:51 CDT)
(no subject) SM Bargeen A Turzo (Wed May 02 2018 - 21:43:45 CDT)
FEP protein-ligand tutorial 2017 unclear section Francesco Pietra (Wed May 02 2018 - 14:51:14 CDT)
Martini CG parameter errors for lipids thiagorrg UFC (Wed May 02 2018 - 12:00:05 CDT)
Re: NAMD Developer Workshop at Urbana IL, June 11-12, 2018 JoÃ£o Ribeiro (Wed May 02 2018 - 09:17:31 CDT)
Re: FEP & node/core number Francesco Pietra (Wed May 02 2018 - 00:53:44 CDT)
Re: Cleaving and capping protein with autopsf leads to parameter errors upon running NAMD Peter Freddolino (Wed May 02 2018 - 00:23:22 CDT)
Cleaving and capping protein with autopsf leads to parameter errors upon running NAMD Jacob Usadi (Wed May 02 2018 - 00:14:40 CDT)
Re: Equilibrated TIP4P_2005 Waterbox Victor Kwan (Tue May 01 2018 - 19:25:34 CDT)
RE: Equilibrated TIP4P_2005 Waterbox Vermaas, Joshua (Tue May 01 2018 - 15:54:14 CDT)
Equilibrated TIP4P_2005 Waterbox Geo Reuter (Tue May 01 2018 - 15:09:53 CDT)
Re: FEP & node/core number Brian Radak (Tue May 01 2018 - 11:58:04 CDT)
FEP & node/core number Francesco Pietra (Mon Apr 30 2018 - 10:36:26 CDT)
Re: Colvars alternative recommendations Giacomo Fiorin (Mon Apr 30 2018 - 10:34:58 CDT)
Re: Colvars alternative recommendations Zachary Ulissi (Mon Apr 30 2018 - 09:50:35 CDT)
Re: Colvars alternative recommendations Giacomo Fiorin (Mon Apr 30 2018 - 09:31:57 CDT)
Re: Energy Minimization failure for mutants JoÃ£o Ribeiro (Mon Apr 30 2018 - 09:24:35 CDT)
Colvars alternative recommendations Zachary Ulissi (Mon Apr 30 2018 - 08:57:27 CDT)
Energy Minimization failure for mutants SM Bargeen A Turzo (Sun Apr 29 2018 - 22:36:54 CDT)
RE: Negative step number Vermaas, Joshua (Sat Apr 28 2018 - 23:07:17 CDT)
Negative step number Bartlomiej Tywoniuk (Sat Apr 28 2018 - 14:03:54 CDT)
Re: water box tilts during equilibration Olya Kravchenko (Fri Apr 27 2018 - 20:31:52 CDT)
RE: water box tilts during equilibration Vermaas, Joshua (Fri Apr 27 2018 - 20:17:10 CDT)
water box tilts during equilibration Olya Kravchenko (Fri Apr 27 2018 - 17:51:39 CDT)
FEP with intermediary segments Francesco Pietra (Thu Apr 26 2018 - 10:20:21 CDT)
Re: Axel Kohlmeyer (Thu Apr 26 2018 - 10:19:18 CDT)
Re: Axel Kohlmeyer (Thu Apr 26 2018 - 10:04:58 CDT)
Re: Giacomo Fiorin (Thu Apr 26 2018 - 09:12:42 CDT)
Re: Brian Radak (Thu Apr 26 2018 - 09:05:49 CDT)
Re: Axel Kohlmeyer (Thu Apr 26 2018 - 08:50:28 CDT)
Re: Giacomo Fiorin (Thu Apr 26 2018 - 08:35:29 CDT)
(no subject) shyam sharma (Thu Apr 26 2018 - 07:02:17 CDT)
Re: Enabling charmrun in NAMD simulation Roshan Shrestha (Wed Apr 25 2018 - 02:11:53 CDT)
Re: Enabling charmrun in NAMD simulation Roshan Shrestha (Wed Apr 25 2018 - 02:10:27 CDT)
Enabling charmrun in NAMD simulation Denish Poudyal (Wed Apr 25 2018 - 01:00:35 CDT)
Setting up amorphous SiO2 slab Carlo Guardiani (Tue Apr 24 2018 - 12:52:20 CDT)
RE: Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available Lennart Nilsson (Tue Apr 24 2018 - 12:45:26 CDT)
RE: Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available Vermaas, Joshua (Tue Apr 24 2018 - 12:08:20 CDT)
Re: Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available Brian Radak (Tue Apr 24 2018 - 11:23:47 CDT)
Re: SMD with colvar not working Dhiraj Srivastava (Tue Apr 24 2018 - 11:12:17 CDT)
Re: SMD with colvar not working Dhiraj Srivastava (Tue Apr 24 2018 - 11:02:29 CDT)
RE: Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available Vermaas, Joshua (Tue Apr 24 2018 - 10:59:35 CDT)
Re: SMD with colvar not working Dhiraj Srivastava (Tue Apr 24 2018 - 10:45:24 CDT)
NAMD Developer Workshop at Urbana IL, June 11-12, 2018 JoÃ£o Ribeiro (Tue Apr 24 2018 - 08:57:57 CDT)
Re: FEP slowdown Francesco Pietra (Tue Apr 24 2018 - 08:51:02 CDT)
Re: vmd-l: PSFGEN 1.6.4 autogenerate PATCH keyword not available Brian Radak (Tue Apr 24 2018 - 07:34:01 CDT)
Re: CZAR Estimator: grad file yjcoshc (Tue Apr 24 2018 - 04:07:20 CDT)
CZAR Estimator: grad file philippe Bourly (Tue Apr 24 2018 - 03:38:49 CDT)
SMD with colvar not working Dhiraj Srivastava (Tue Apr 24 2018 - 00:21:43 CDT)
PSFGEN 1.6.4 autogenerate PATCH keyword not available Thomas C. Bishop (Mon Apr 23 2018 - 19:57:47 CDT)
Re: Question about "useConstantArea" in puresure control model Brian Radak (Mon Apr 23 2018 - 11:20:26 CDT)
Re: How to interpret Thermodynamic Integration output Sadegh Faramarzi Ganjabad (Mon Apr 23 2018 - 11:01:02 CDT)
RE: Question about "useConstantArea" in puresure control model Vermaas, Joshua (Mon Apr 23 2018 - 10:54:23 CDT)
Re: Question about "useConstantArea" in puresure control model Brian Radak (Mon Apr 23 2018 - 07:38:42 CDT)
Re: FEP slowdown Brian Radak (Mon Apr 23 2018 - 07:34:47 CDT)
RE: Question about "useConstantArea" in puresure control model Vermaas, Joshua (Sat Apr 21 2018 - 13:49:08 CDT)
Question about "useConstantArea" in puresure control model å¼ é”¦é€” (Sat Apr 21 2018 - 11:00:31 CDT)
FEP slowdown Francesco Pietra (Sat Apr 21 2018 - 10:34:58 CDT)
RE: long simulation and error "integer value too large" dhirajks (Sat Apr 21 2018 - 09:04:42 CDT)
RE: long simulation and error "integer value too large" Vermaas, Joshua (Sat Apr 21 2018 - 08:45:51 CDT)
long simulation and error "integer value too large" Dhiraj Srivastava (Fri Apr 20 2018 - 23:24:23 CDT)
RE: torsion scan Vermaas, Joshua (Thu Apr 19 2018 - 18:49:48 CDT)
torsion scan Stefano Guglielmo (Thu Apr 19 2018 - 18:30:00 CDT)
Re: How to interpret Thermodynamic Integration output Brian Radak (Thu Apr 19 2018 - 09:15:32 CDT)
variation of pressure Suresh Ghimire (Thu Apr 19 2018 - 05:31:57 CDT)
Re: How to interpret Thermodynamic Integration output Sadegh Faramarzi Ganjabad (Wed Apr 18 2018 - 14:57:56 CDT)
Re: Meaning of warning in output log file Victor Kwan (Tue Apr 17 2018 - 14:10:33 CDT)
Re: colvar with moving frame of reference Dhiraj Srivastava (Tue Apr 17 2018 - 13:39:23 CDT)
Re: Reverting coarse-grain system to all-atom system Rabeta Yeasmin (Tue Apr 17 2018 - 10:49:55 CDT)
Re: vmd-l: Re: Re: Bug with FEP? Brian Radak (Tue Apr 17 2018 - 09:42:46 CDT)
Re: vmd-l: Re: Re: Bug with FEP? Francesco Pietra (Tue Apr 17 2018 - 00:05:38 CDT)
Re: Reverting coarse-grain system to all-atom system Peter Freddolino (Mon Apr 16 2018 - 16:05:39 CDT)
Re: colvar with moving frame of reference Giacomo Fiorin (Mon Apr 16 2018 - 15:03:08 CDT)
Re: colvar with moving frame of reference Dhiraj Srivastava (Mon Apr 16 2018 - 14:24:41 CDT)
RE: colvar with moving frame of reference Vermaas, Joshua (Mon Apr 16 2018 - 14:08:06 CDT)
colvar with moving frame of reference Dhiraj Srivastava (Mon Apr 16 2018 - 13:29:53 CDT)
Re: vmd-l: Re: Re: Bug with FEP? Brian Radak (Mon Apr 16 2018 - 11:31:45 CDT)
Re: Reverting coarse-grain system to all-atom system Peter Freddolino (Mon Apr 16 2018 - 10:43:49 CDT)
Re: Reverting coarse-grain system to all-atom system Rabeta Yeasmin (Mon Apr 16 2018 - 10:41:11 CDT)
Re: Reverting coarse-grain system to all-atom system Peter Freddolino (Sun Apr 15 2018 - 19:57:33 CDT)
Reverting coarse-grain system to all-atom system Rabeta Yeasmin (Sun Apr 15 2018 - 18:49:21 CDT)
Re: Re: Bug with FEP? Francesco Pietra (Sun Apr 15 2018 - 02:48:10 CDT)
Re: re-centering the molecule while restarting the run Dawid das (Fri Apr 13 2018 - 15:18:06 CDT)
re-centering the molecule while restarting the run Dhiraj Srivastava (Fri Apr 13 2018 - 13:27:30 CDT)
Re: Re: Bug with FEP? Brian Radak (Fri Apr 13 2018 - 10:03:17 CDT)
Re: Bug with FEP? Francesco Pietra (Fri Apr 13 2018 - 02:49:14 CDT)
Re: How does NAMD calculate AccumulatedWork when using RMSD colvar? Giacomo Fiorin (Thu Apr 12 2018 - 16:14:53 CDT)
Bug with FEP? Francesco Pietra (Thu Apr 12 2018 - 15:28:31 CDT)
Re: How does NAMD calculate AccumulatedWork when using RMSD colvar? Giacomo Fiorin (Thu Apr 12 2018 - 14:54:13 CDT)
Re: How does NAMD calculate AccumulatedWork when using RMSD colvar? Giacomo Fiorin (Thu Apr 12 2018 - 14:49:04 CDT)
How does NAMD calculate AccumulatedWork when using RMSD colvar? Asghar Razavi (Thu Apr 12 2018 - 12:29:19 CDT)
Re: scriptedColvarForces doesn't work in recent NAMD builds Giacomo Fiorin (Thu Apr 12 2018 - 11:55:59 CDT)
Re: scriptedColvarForces doesn't work in recent NAMD builds Jeff Comer (Thu Apr 12 2018 - 08:14:26 CDT)
Re: scriptedColvarForces doesn't work in recent NAMD builds Giacomo Fiorin (Wed Apr 11 2018 - 15:09:13 CDT)
Re: RE: Regarding Topology and Parameterization SM Bargeen A Turzo (Wed Apr 11 2018 - 14:25:22 CDT)
Re: RE: Regarding Topology and Parameterization SM Bargeen A Turzo (Wed Apr 11 2018 - 14:16:12 CDT)
Re: RE: Regarding Topology and Parameterization JC Gumbart (Wed Apr 11 2018 - 13:12:32 CDT)
scriptedColvarForces doesn't work in recent NAMD builds Jeff Comer (Wed Apr 11 2018 - 11:04:53 CDT)
RE: Regarding Topology and Parameterization Vermaas, Joshua (Wed Apr 11 2018 - 11:02:35 CDT)
Re: Query for coarse grain system Abhishek TYAGI (Wed Apr 11 2018 - 00:39:49 CDT)
Regarding Topology and Parameterization SM Bargeen A Turzo (Tue Apr 10 2018 - 18:51:35 CDT)
Re: Re: Bad global bond count! (48842 vs 48843) Brian Radak (Tue Apr 10 2018 - 12:50:45 CDT)
Re: Bad global bond count! (48842 vs 48843) Ashutosh Shandilya (Tue Apr 10 2018 - 11:41:32 CDT)
Re: Proper use of psfgen "mutate"? Brian Radak (Tue Apr 10 2018 - 09:41:54 CDT)
Re: vmd-l: Proper use of psfgen "mutate"? Francesco Pietra (Tue Apr 10 2018 - 09:20:20 CDT)
Proper use of psfgen "mutate"? Brian Radak (Tue Apr 10 2018 - 08:58:47 CDT)
Re: ParseFEP error with FEP in segments at different lambda schedule Brian Radak (Tue Apr 10 2018 - 07:56:40 CDT)
Re: Query for coarse grain system Abhishek TYAGI (Mon Apr 09 2018 - 12:17:06 CDT)
Re: calculation of helical axis in NAMD Dhiraj Srivastava (Mon Apr 09 2018 - 10:29:11 CDT)
Re: Query for coarse grain system Axel Kohlmeyer (Mon Apr 09 2018 - 09:22:11 CDT)
Re: Query for coarse grain system Giacomo Fiorin (Mon Apr 09 2018 - 09:02:23 CDT)
Re: Query for coarse grain system Abhishek TYAGI (Mon Apr 09 2018 - 08:42:35 CDT)
Re: colvars: make an extended CV periodic yjcoshc_at_gmail.com (Mon Apr 09 2018 - 08:22:31 CDT)
RE: calculation of helical axis in NAMD Vermaas, Joshua (Sun Apr 08 2018 - 18:28:10 CDT)
Re: calculation of helical axis in NAMD Dhiraj Srivastava (Sun Apr 08 2018 - 17:41:48 CDT)
Re: TCBG Workshop lecture videosðŸ˜ðŸ˜šðŸ˜š è‘£è¶… (Sun Apr 08 2018 - 14:21:02 CDT)
Re: ParseFEP error with FEP in segments at different lambda schedule Chris Chipot (Sun Apr 08 2018 - 08:58:34 CDT)
ParseFEP error with FEP in segments at different lambda schedule Francesco Pietra (Sun Apr 08 2018 - 08:46:35 CDT)
TCBG Workshop lecture videos JoÃ£o Ribeiro (Sat Apr 07 2018 - 10:45:12 CDT)
RE: calculation of helical axis in NAMD Vermaas, Joshua (Sat Apr 07 2018 - 10:01:45 CDT)
Re: Selective accelerated MD in NAMD Chitrak Gupta (Sat Apr 07 2018 - 09:42:25 CDT)
Re: Selective accelerated MD in NAMD Alexander Adams (Sat Apr 07 2018 - 07:00:37 CDT)
calculation of helical axis in NAMD Dhiraj Srivastava (Sat Apr 07 2018 - 01:01:20 CDT)
Re: colvars: make an extended CV periodic yjcoshc_at_gmail.com (Fri Apr 06 2018 - 21:21:12 CDT)
Re: Selective accelerated MD in NAMD Chitrak Gupta (Fri Apr 06 2018 - 17:42:15 CDT)
Re: Selective accelerated MD in NAMD Alexander Adams (Fri Apr 06 2018 - 15:36:59 CDT)
Selective accelerated MD in NAMD Alexander Adams (Fri Apr 06 2018 - 14:08:43 CDT)
Re: colvars: make an extended CV periodic Giacomo Fiorin (Fri Apr 06 2018 - 13:05:07 CDT)
CMIAbort Error Harish Srinivasan (Fri Apr 06 2018 - 05:38:39 CDT)
colvars: make an extended CV periodic yjcoshc (Thu Apr 05 2018 - 22:42:01 CDT)
Re: NAMD-CUDA GPU workload Lewis J Martin (Thu Apr 05 2018 - 19:50:09 CDT)
Re: Query for coarse grain system Giacomo Fiorin (Thu Apr 05 2018 - 10:27:16 CDT)
Re: Query for coarse grain system Abhishek TYAGI (Thu Apr 05 2018 - 10:23:18 CDT)
Re: Query for coarse grain system Giacomo Fiorin (Thu Apr 05 2018 - 10:17:47 CDT)
Query for coarse grain system Abhishek TYAGI (Thu Apr 05 2018 - 09:53:36 CDT)
Re: Fatty Acid Topology Fotis Baltoumas (Mon Apr 02 2018 - 12:46:54 CDT)
Re: NAMD-CUDA GPU workload David Hardy (Mon Apr 02 2018 - 11:33:06 CDT)
Re: Steered MD simulation with pull and rotation Giacomo Fiorin (Mon Apr 02 2018 - 10:40:56 CDT)
Re: Using restraint on the dye using radius of gyration value in namd Giacomo Fiorin (Mon Apr 02 2018 - 10:40:18 CDT)
NAMD-CUDA GPU workload Yu Zhou (Mon Apr 02 2018 - 10:11:51 CDT)
Using restraint on the dye using radius of gyration value in namd Life Sciences Inc (Mon Apr 02 2018 - 09:26:47 CDT)
Re: Steered MD simulation with pull and rotation Dhiraj Srivastava (Mon Apr 02 2018 - 09:24:36 CDT)
Re: Fatty Acid Topology Jeff Comer (Mon Apr 02 2018 - 09:14:32 CDT)
effect of acceptors Suresh Ghimire (Sun Apr 01 2018 - 10:44:37 CDT)
Re: Fatty Acid Topology Brian Radak (Sun Apr 01 2018 - 09:01:48 CDT)
Re: Atom velocity error in coarse grained simulation using MARTINI Fotis Baltoumas (Sun Apr 01 2018 - 06:07:58 CDT)
Atom velocity error in coarse grained simulation using MARTINI Rakesh K (Sat Mar 31 2018 - 10:16:39 CDT)
Fatty Acid Topology Nisler, Collin R. (Fri Mar 30 2018 - 21:25:30 CDT)
Re: Steered MD simulation with pull and rotation Giacomo Fiorin (Thu Mar 29 2018 - 06:37:55 CDT)
Re: Using PBC tools for a cubic and a rectangular box Monika Madhavi (Wed Mar 28 2018 - 23:07:41 CDT)
Steered MD simulation with pull and rotation Dhiraj Srivastava (Wed Mar 28 2018 - 14:23:08 CDT)
Re: Meaning of warning in output log file Vermaas, Joshua (Wed Mar 28 2018 - 09:53:41 CDT)
Meaning of warning in output log file Denish Poudyal (Wed Mar 28 2018 - 02:57:23 CDT)
Re: Using PBC tools for a cubic and a rectangular box Giacomo Fiorin (Tue Mar 27 2018 - 09:18:17 CDT)
Re: Using PBC tools for a cubic and a rectangular box Brian Radak (Tue Mar 27 2018 - 09:03:55 CDT)
Re: Using PBC tools for a cubic and a rectangular box Giacomo Fiorin (Tue Mar 27 2018 - 08:35:54 CDT)
Re: Using PBC tools for a cubic and a rectangular box Brian Radak (Tue Mar 27 2018 - 08:09:43 CDT)
Using PBC tools for a cubic and a rectangular box Monika Madhavi (Tue Mar 27 2018 - 05:34:10 CDT)
Re: NAMD Simulation in a laptop Vermaas, Joshua (Mon Mar 26 2018 - 13:42:06 CDT)
metadynamics problem Rabeta Yeasmin (Mon Mar 26 2018 - 11:39:28 CDT)
Restrict drift of Graphene sheet in X-Y plane using Colvars ANIRBAN MANDAL (Mon Mar 26 2018 - 05:04:55 CDT)
Regarding free energy calculation varun dewaker (Mon Mar 26 2018 - 02:39:54 CDT)
Re: NAMD Simulation in a laptop Denish Poudyal (Sun Mar 25 2018 - 23:34:38 CDT)
Re: NAMD Simulation in a laptop Richard Overstreet (Sun Mar 25 2018 - 23:26:24 CDT)
Re: NAMD Simulation in a laptop Denish Poudyal (Sun Mar 25 2018 - 21:37:28 CDT)
Re: NAMD Simulation in a laptop Axel Kohlmeyer (Sun Mar 25 2018 - 21:07:13 CDT)
NAMD Simulation in a laptop Denish Poudyal (Sun Mar 25 2018 - 20:56:44 CDT)
Re: vmd-l: [VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin The Cromicus Productions (Sun Mar 25 2018 - 20:31:45 CDT)
Re: vmd-l: Fwd: ParseFEP for restating FEP Francesco Pietra (Fri Mar 23 2018 - 15:31:58 CDT)
Re: vmd-l: [VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin Brian Radak (Fri Mar 23 2018 - 10:59:05 CDT)
Re: vmd-l: Fwd: ParseFEP for restating FEP Brian Radak (Fri Mar 23 2018 - 10:48:17 CDT)
Re: How to interpret Thermodynamic Integration output Brian Radak (Fri Mar 23 2018 - 10:30:26 CDT)
Fwd: ParseFEP for restating FEP Francesco Pietra (Fri Mar 23 2018 - 09:00:15 CDT)
ParseFEP for restating FEP Francesco Pietra (Fri Mar 23 2018 - 02:05:41 CDT)
[VMD-NAMD] Question about Dipole of DNA / Dipole Moment Watcher Plugin The Cromicus Productions (Thu Mar 22 2018 - 18:17:30 CDT)
Re: How to interpret Thermodynamic Integration output Sadegh Faramarzi Ganjabad (Thu Mar 22 2018 - 14:13:03 CDT)
patch ID error deep deep (Wed Mar 21 2018 - 15:18:04 CDT)
Re: Selecting waters from dynamics trajectory Randy J. Zauhar (Wed Mar 21 2018 - 11:08:46 CDT)
Re: colvars: Questions about the metadynamics hillWIdth option. Giacomo Fiorin (Wed Mar 21 2018 - 08:55:11 CDT)
colvars: Questions about the metadynamics hillWIdth option. yjcoshc (Wed Mar 21 2018 - 02:39:09 CDT)
Re: Selecting waters from dynamics trajectory Giacomo Fiorin (Tue Mar 20 2018 - 17:05:43 CDT)
Selecting waters from dynamics trajectory Randy J. Zauhar (Tue Mar 20 2018 - 16:47:38 CDT)
Re: ffTK Without Using Gaussian Giacomo Fiorin (Tue Mar 20 2018 - 15:43:43 CDT)
Re: ffTK Without Using Gaussian Ajasja LjubetiÄ (Tue Mar 20 2018 - 15:35:40 CDT)
Re: ffTK Without Using Gaussian JC Gumbart (Tue Mar 20 2018 - 14:37:35 CDT)
Re: ffTK Without Using Gaussian Fotis Baltoumas (Tue Mar 20 2018 - 12:59:34 CDT)
ffTK Without Using Gaussian Alex Saad-Falcon (Tue Mar 20 2018 - 10:49:48 CDT)
Re: JC Gumbart (Mon Mar 19 2018 - 19:13:33 CDT)
Re: Srijita Paul (Mon Mar 19 2018 - 14:54:36 CDT)
Re: Srijita Paul (Mon Mar 19 2018 - 14:54:36 CDT)
Re: Giacomo Fiorin (Mon Mar 19 2018 - 08:08:23 CDT)
Re: Brian Radak (Mon Mar 19 2018 - 07:58:36 CDT)
Re: statistical error in ABF calculations Giacomo Fiorin (Mon Mar 19 2018 - 06:35:42 CDT)
Re: Srijita Paul (Mon Mar 19 2018 - 04:16:13 CDT)
Re: Brian Radak (Sun Mar 18 2018 - 15:27:05 CDT)
VMD/NMAD on AWS Strenic Computations (Sat Mar 17 2018 - 18:50:17 CDT)
Re: Artur Hermano (Sat Mar 17 2018 - 16:41:44 CDT)
"'Hands-on" Workshop on Computational Biophysics at Pittsburgh, PA, May 21-25, 2018 JoÃ£o Ribeiro (Fri Mar 16 2018 - 15:47:15 CDT)
(no subject) Srijita Paul (Fri Mar 16 2018 - 14:14:22 CDT)
Lowe-Andersen Thermostat Speed Nick Guros (Fri Mar 16 2018 - 13:59:43 CDT)
Re: Brian Radak (Fri Mar 16 2018 - 09:26:38 CDT)
(no subject) Srijita Paul (Fri Mar 16 2018 - 06:40:03 CDT)
(no subject) Srijita Paul (Fri Mar 16 2018 - 05:54:30 CDT)
Re: statistical error in ABF calculations Giacomo Fiorin (Thu Mar 15 2018 - 20:04:38 CDT)
Re: Brian Radak (Thu Mar 15 2018 - 08:24:07 CDT)
(no subject) Srijita Paul (Thu Mar 15 2018 - 06:44:21 CDT)
statistical error in ABF calculations Artur Hermano (Wed Mar 14 2018 - 10:27:15 CDT)
Re: colvars: How to implement a collective variable of vector type? Giacomo Fiorin (Wed Mar 14 2018 - 08:26:48 CDT)
Re: colvars: How to implement a collective variable of vector type? yjcoshc (Wed Mar 14 2018 - 04:13:19 CDT)
mscs.pdb Mahmood Naderan (Tue Mar 13 2018 - 11:03:33 CDT)
Re: colvars: How to implement a collective variable of vector type? Giacomo Fiorin (Tue Mar 13 2018 - 09:07:18 CDT)
AW: Low global CUDA exclusion count! (9592 vs 9618) Norman Geist (Tue Mar 13 2018 - 06:05:46 CDT)
AW: Low global CUDA exclusion count! (9592 vs 9618) Norman Geist (Tue Mar 13 2018 - 05:56:25 CDT)
Low global CUDA exclusion count! (9592 vs 9618) ANIRBAN MANDAL (Tue Mar 13 2018 - 04:39:31 CDT)
Re: colvars: How to implement a collective variable of vector type? yjcoshc (Tue Mar 13 2018 - 03:12:51 CDT)
Re: Running on GPU Mahmood Naderan (Mon Mar 12 2018 - 14:47:35 CDT)
Re: Running on GPU Vermaas, Joshua (Mon Mar 12 2018 - 14:46:57 CDT)
Re: Running on GPU Bassam Haddad (Mon Mar 12 2018 - 14:33:58 CDT)
Running on GPU Mahmood Naderan (Mon Mar 12 2018 - 14:22:31 CDT)
Re: AutoPSF Error Peter Freddolino (Mon Mar 12 2018 - 12:22:35 CDT)
AutoPSF Error Alex Saad-Falcon (Mon Mar 12 2018 - 10:40:47 CDT)
Re: colvars: How to implement a collective variable of vector type? Giacomo Fiorin (Mon Mar 12 2018 - 07:13:52 CDT)
Re: colvars: How to implement a collective variable of vector type? yjcoshc (Mon Mar 12 2018 - 05:01:52 CDT)
Re: colvars: How to implement a collective variable of vector type? yjcoshc (Mon Mar 12 2018 - 02:32:56 CDT)
Re: colvars: How to implement a collective variable of vector type? JÃ©rÃ´me HÃ©nin (Sun Mar 11 2018 - 16:54:15 CDT)
Re: colvars: How to implement a collective variable of vector type? Giacomo Fiorin (Sun Mar 11 2018 - 07:05:09 CDT)
colvars: How to implement a collective variable of vector type? yjcoshc (Sat Mar 10 2018 - 03:27:54 CST)
Re: Python based tool for analysis of DCD trajectories Vermaas, Joshua (Fri Mar 09 2018 - 12:28:42 CST)
Re: Python based tool for analysis of DCD trajectories Brian Radak (Fri Mar 09 2018 - 08:41:16 CST)
(no subject) shyam sharma (Fri Mar 09 2018 - 02:02:09 CST)
Re: Python based tool for analysis of DCD trajectories Haohao Fu (Fri Mar 09 2018 - 00:52:15 CST)
Python based tool for analysis of DCD trajectories Harish Srinivasan (Thu Mar 08 2018 - 23:46:32 CST)
Re: Hydrogen Mass Repartitioning in NAMD JC Gumbart (Thu Mar 08 2018 - 09:36:43 CST)
Re: Hydrogen Mass Repartitioning in NAMD Brian Radak (Thu Mar 08 2018 - 09:00:04 CST)
AW: Hydrogen Mass Repartitioning in NAMD Norman Geist (Thu Mar 08 2018 - 08:53:24 CST)
Re: Hydrogen Mass Repartitioning in NAMD Brian Radak (Thu Mar 08 2018 - 08:44:24 CST)
Re: Functionality of wrapWater and wrapAll commands for periodic simulations Harish Srinivasan (Wed Mar 07 2018 - 23:11:19 CST)
Hydrogen Mass Repartitioning in NAMD JC Gumbart (Wed Mar 07 2018 - 17:31:32 CST)
Re: Segmentation fault for the tutorial Mahmood Naderan (Wed Mar 07 2018 - 14:24:31 CST)
Re: Segmentation fault for the tutorial Vermaas, Joshua (Wed Mar 07 2018 - 12:30:36 CST)
Re: Segmentation fault for the tutorial Mahmood Naderan (Wed Mar 07 2018 - 12:02:02 CST)
Re: Segmentation fault for the tutorial Mahmood Naderan (Wed Mar 07 2018 - 11:38:44 CST)
Re: Segmentation fault for the tutorial David Hardy (Wed Mar 07 2018 - 10:51:44 CST)
Re: Segmentation fault for the tutorial Mahmood Naderan (Wed Mar 07 2018 - 09:48:08 CST)
Re: Fwd: parseFEP domain error Francesco Pietra (Wed Mar 07 2018 - 08:39:49 CST)
Re: Thermodynamic integration output analysis Brian Radak (Wed Mar 07 2018 - 07:59:18 CST)
Re: Functionality of wrapWater and wrapAll commands for periodic simulations Giacomo Fiorin (Wed Mar 07 2018 - 07:35:30 CST)
Thermodynamic integration output analysis Giorgio Amendola (Wed Mar 07 2018 - 05:57:08 CST)
Functionality of wrapWater and wrapAll commands for periodic simulations Harish Srinivasan (Wed Mar 07 2018 - 05:34:08 CST)
Re: Segmentation fault for the tutorial Mahmood Naderan (Wed Mar 07 2018 - 01:33:55 CST)
Re: periodic cell has become too small for original patch grid Vermaas, Joshua (Tue Mar 06 2018 - 15:53:00 CST)
Re: periodic cell has become too small for original patch grid Ashutosh Shandilya (Tue Mar 06 2018 - 15:41:54 CST)
Re: Segmentation fault for the tutorial Vermaas, Joshua (Tue Mar 06 2018 - 14:27:43 CST)
Re: Segmentation fault for the tutorial Mahmood Naderan (Tue Mar 06 2018 - 13:58:56 CST)
Segmentation fault for the tutorial Mahmood Naderan (Tue Mar 06 2018 - 13:06:11 CST)
Re: Simulating a Binding Event Lutimba Stuart (Tue Mar 06 2018 - 12:44:52 CST)
Simulating a Binding Event Alex Saad-Falcon (Tue Mar 06 2018 - 11:53:54 CST)
AW: periodic cell has become too small for original patch grid Norman Geist (Tue Mar 06 2018 - 01:50:42 CST)
Re: Fwd: parseFEP domain error Chris Chipot (Mon Mar 05 2018 - 17:25:57 CST)
Re: vmd-l: Fwd: parseFEP domain error Brian Radak (Mon Mar 05 2018 - 15:43:15 CST)
Fwd: parseFEP domain error Francesco Pietra (Mon Mar 05 2018 - 14:17:56 CST)
Ph.D. and Post-doc positions in molecular simulations and structural bioinformatics Jan Brezovsky (Mon Mar 05 2018 - 11:10:28 CST)
Re: Re: How to set up a window distance of 2 angstroms in Umbrella sampling Giacomo Fiorin (Mon Mar 05 2018 - 07:38:59 CST)
Re: How to set up a window distance of 2 angstroms in Umbrella sampling Lutimba Stuart (Mon Mar 05 2018 - 03:40:10 CST)
AW: periodic cell has become too small for original patch grid Norman Geist (Mon Mar 05 2018 - 02:17:25 CST)
Fwd: parseFEP domain error Francesco Pietra (Sat Mar 03 2018 - 11:44:06 CST)
Re: Build for CUDA support Mahmood Naderan (Sat Mar 03 2018 - 10:35:06 CST)
Re: Build for CUDA support Giacomo Fiorin (Sat Mar 03 2018 - 10:10:35 CST)
Re: Build for CUDA support Renfro, Michael (Sat Mar 03 2018 - 10:03:26 CST)
Build for CUDA support Mahmood Naderan (Sat Mar 03 2018 - 08:22:47 CST)
Re: UNABLE TO FIND ANGLE PARAMETERS FOR CT OS HO (ATOMS 23662 23661 23656) Brian Radak (Fri Mar 02 2018 - 14:29:26 CST)
UNABLE TO FIND ANGLE PARAMETERS FOR CT OS HO (ATOMS 23662 23661 23656) Ashutosh Shandilya (Fri Mar 02 2018 - 13:55:43 CST)
periodic cell has become too small for original patch grid Ashutosh Shandilya (Fri Mar 02 2018 - 13:55:10 CST)
Re: Residue Charges Ajasja LjubetiÄ (Fri Mar 02 2018 - 08:55:31 CST)
Re: Residue Charges Sharp, Kim (Fri Mar 02 2018 - 08:49:05 CST)
Residue Charges Alex Saad-Falcon (Fri Mar 02 2018 - 08:35:30 CST)
Re: FEP minimum requirements Brian Radak (Thu Mar 01 2018 - 08:18:27 CST)
FEP minimum requirements Francesco Pietra (Thu Mar 01 2018 - 03:05:22 CST)
Re: How to interpret Thermodynamic Integration output Brian Radak (Tue Feb 27 2018 - 13:00:48 CST)
Re: How to interpret Thermodynamic Integration output Sadegh Faramarzi Ganjabad (Tue Feb 27 2018 - 12:26:17 CST)
Re: "Hands-On" Workshop on QM/MM Simulations at Urbana, IL, April 5-7, 2018 JoÃ£o Ribeiro (Tue Feb 27 2018 - 08:08:16 CST)
Re: How to interpret Thermodynamic Integration output Vermaas, Joshua (Sun Feb 25 2018 - 17:23:39 CST)
Handling of nonbonded lists in PSF - please clarify Randy J. Zauhar (Sun Feb 25 2018 - 14:42:10 CST)
Re: How to interpret Thermodynamic Integration output Brian Radak (Sun Feb 25 2018 - 12:45:10 CST)
Re: Coarse-grained umbrella sampling for POPS-protein system JC Gumbart (Sat Feb 24 2018 - 08:39:07 CST)
parameter Suresh Ghimire (Sat Feb 24 2018 - 07:40:24 CST)
How to interpret Thermodynamic Integration output Sadegh Faramarzi Ganjabad (Fri Feb 23 2018 - 18:09:19 CST)
Re: Coarse-grained umbrella sampling for POPS-protein system Lutimba Stuart (Fri Feb 23 2018 - 18:02:53 CST)
Coarse-grained umbrella sampling for POPS-protein system Rabeta Yeasmin (Fri Feb 23 2018 - 17:53:53 CST)
Re: Error in the Continuation TMD simulation Run. Lutimba Stuart (Wed Feb 21 2018 - 13:49:36 CST)
Re: colvars selecting frames Stefano Guglielmo (Tue Feb 20 2018 - 14:54:20 CST)
Re: Ligand atoms moving too fast with FEP Brian Radak (Tue Feb 20 2018 - 10:21:48 CST)
Re: Ligand atoms moving too fast with FEP Francesco Pietra (Tue Feb 20 2018 - 10:10:50 CST)
Re: Ligand atoms moving too fast with FEP Brian Radak (Tue Feb 20 2018 - 09:24:04 CST)
Fwd: Ligand atoms moving too fast with FEP Francesco Pietra (Tue Feb 20 2018 - 09:23:05 CST)
RE: namd2 GPU error Miraj Naik (Tue Feb 20 2018 - 05:22:16 CST)
Fwd: Ligand atoms moving too fast with FEP Francesco Pietra (Tue Feb 20 2018 - 02:08:17 CST)
Fwd: Ligand atoms moving too fast with FEP Francesco Pietra (Tue Feb 20 2018 - 01:58:37 CST)
Re: Question on making 'reversible' solvated simulation Randy J. Zauhar (Mon Feb 19 2018 - 12:42:36 CST)
Re: Simple PME Question Brian Radak (Mon Feb 19 2018 - 11:04:12 CST)
Re: PME Tolerance Brian Radak (Mon Feb 19 2018 - 11:02:23 CST)
Re: Question on making 'reversible' solvated simulation Brian Radak (Mon Feb 19 2018 - 11:00:20 CST)
Simple PME Question Alex Saad-Falcon (Mon Feb 19 2018 - 10:04:54 CST)
PME Tolerance Lesli Oiling Mark (Mon Feb 19 2018 - 10:03:48 CST)
Re: FAD topology and parameters Aashish Bhatt (Mon Feb 19 2018 - 09:46:16 CST)
FAD topology and parameters Marco kadowaki (Mon Feb 19 2018 - 09:23:53 CST)
Re: Question on making 'reversible' solvated simulation Randy J. Zauhar (Sun Feb 18 2018 - 17:01:27 CST)
Re: Question on making 'reversible' solvated simulation Randy J. Zauhar (Sun Feb 18 2018 - 16:54:20 CST)
Re: Vermaas, Joshua (Sun Feb 18 2018 - 12:09:02 CST)
ParseFEP error Sadegh Faramarzi Ganjabad (Sat Feb 17 2018 - 23:39:52 CST)
Re: Question on making 'reversible' solvated simulation Randy J. Zauhar (Sat Feb 17 2018 - 11:20:48 CST)
Re: Ligand atoms moving too fast with FEP Francesco Pietra (Fri Feb 16 2018 - 09:31:08 CST)
Re: Ligand atoms moving too fast with FEP Brian Radak (Fri Feb 16 2018 - 07:47:18 CST)
Re: Srijita Paul (Fri Feb 16 2018 - 06:42:56 CST)
Re: Ligand atoms moving too fast with FEP Francesco Pietra (Thu Feb 15 2018 - 09:47:51 CST)
Re: Ligand atoms moving too fast with FEP Brian Radak (Thu Feb 15 2018 - 08:27:42 CST)
Ligand atoms moving too fast with FEP Francesco Pietra (Thu Feb 15 2018 - 02:00:39 CST)
Re: namd2 GPU error Vermaas, Joshua (Wed Feb 14 2018 - 12:14:28 CST)
Re: namd2 GPU error Giacomo Fiorin (Wed Feb 14 2018 - 08:32:21 CST)
namd2 GPU error Miraj Naik (Tue Feb 13 2018 - 22:43:10 CST)
Re: Vermaas, Joshua (Tue Feb 13 2018 - 13:41:42 CST)
Re: Re: simulation becomes unstable in residue base coarse grained system Shahee Islam (Tue Feb 13 2018 - 06:56:10 CST)
Re: Souvik Sinha (Tue Feb 13 2018 - 06:32:42 CST)
Re: Re: simulation becomes unstable in residue base coarse grained system Fotis Baltoumas (Tue Feb 13 2018 - 06:13:14 CST)
Re: Re: simulation becomes unstable in residue base coarse grained system Shahee Islam (Tue Feb 13 2018 - 05:53:23 CST)
(no subject) Srijita Paul (Tue Feb 13 2018 - 05:06:51 CST)
Re: Question on making 'reversible' solvated simulation Brian Radak (Mon Feb 12 2018 - 10:00:18 CST)
Re: Re: simulation becomes unstable in residue base coarse grained system Shahee Islam (Mon Feb 12 2018 - 09:27:03 CST)
Re: Re: simulation becomes unstable in residue base coarse grained system Giacomo Fiorin (Mon Feb 12 2018 - 09:20:04 CST)
Re: Re: simulation becomes unstable in residue base coarse grained system SHAHEE ISLAM (Mon Feb 12 2018 - 09:05:04 CST)
Re: Re: simulation becomes unstable in residue base coarse grained system Giacomo Fiorin (Mon Feb 12 2018 - 08:38:15 CST)
Re: simulation becomes unstable in residue base coarse grained system Shahee Islam (Sun Feb 11 2018 - 23:08:42 CST)
Ph.D. and Post-doc positions in molecular simulations and structural bioinformatics Jan Brezovsky (Sun Feb 11 2018 - 15:59:31 CST)
Re: Question on making 'reversible' solvated simulation Randy J. Zauhar (Sun Feb 11 2018 - 12:52:18 CST)
Question on making 'reversible' solvated simulation Randy J. Zauhar (Sat Feb 10 2018 - 12:15:37 CST)
Re: Dielectric Constant in the gas phase Brian Radak (Fri Feb 09 2018 - 13:15:16 CST)
Re: Dielectric Constant in the gas phase Giacomo Fiorin (Fri Feb 09 2018 - 12:19:09 CST)
Re: Dielectric Constant in the gas phase Vermaas, Joshua (Fri Feb 09 2018 - 12:18:33 CST)
Dielectric Constant in the gas phase Ahmad Kiani (Fri Feb 09 2018 - 11:47:08 CST)
Lipid bilayer deformed during coarse grain simulation Rabeta Yeasmin (Fri Feb 09 2018 - 10:58:19 CST)
Re: Pair interaction energies: TCL error -reg Souvik Sinha (Thu Feb 08 2018 - 07:32:26 CST)
Pair interaction energies: TCL error -reg Jeyaram R A (Thu Feb 08 2018 - 01:32:44 CST)
Re: Double-defined segid, resid for more than 9999 id's Chun Heung Wong (Wed Feb 07 2018 - 10:59:28 CST)
"Hands-on" Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL, September 10-14, 2018 JoÃ£o Ribeiro (Wed Feb 07 2018 - 10:46:51 CST)
NAMD Developer Workshop at Urbana IL, June 11-12, 2018 JoÃ£o Ribeiro (Wed Feb 07 2018 - 10:46:41 CST)
"Hands-On" Workshop on QM/MM Simulations at Urbana, IL, April 5-7, 2018 JoÃ£o Ribeiro (Wed Feb 07 2018 - 10:44:57 CST)
FEP/REMD (ERROR: 'alchLambda' is a required configuration option) rakesh kumar (Wed Feb 07 2018 - 03:25:17 CST)
Re: NAMD run on Intel hyperthreaded cores Souvik Sinha (Tue Feb 06 2018 - 14:17:50 CST)
Re: NAMD run on Intel hyperthreaded cores Giacomo Fiorin (Tue Feb 06 2018 - 13:54:50 CST)
Re: NAMD run on Intel hyperthreaded cores Souvik Sinha (Tue Feb 06 2018 - 08:20:43 CST)
NAMD run on Intel hyperthreaded cores Souvik Sinha (Tue Feb 06 2018 - 02:41:49 CST)
Jobs and Evens in CHARMM-GUI Jumin Lee (Mon Feb 05 2018 - 16:00:01 CST)
Re: all-atom to coarse-grained system Rabeta Yeasmin (Mon Feb 05 2018 - 11:23:20 CST)
Re: Holding molecules on one side of membrane Vermaas, Joshua (Mon Feb 05 2018 - 11:18:56 CST)
QwikMD SMD force calculation Aysima Hacisuleyman (Mon Feb 05 2018 - 04:00:02 CST)
Re: Calculate energy of a residue using NAMD energy Peter Freddolino (Mon Feb 05 2018 - 00:42:43 CST)
Re: Holding molecules on one side of membrane Giacomo Fiorin (Sun Feb 04 2018 - 09:07:30 CST)
Holding molecules on one side of membrane Omid Bavi (Sun Feb 04 2018 - 07:14:26 CST)
Re: all-atom to coarse-grained system Marlon Sidore (Sat Feb 03 2018 - 14:04:34 CST)
NAMD 2.12 Volta Compatibility Richard Overstreet (Sat Feb 03 2018 - 13:24:45 CST)
Re: all-atom to coarse-grained system Vermaas, Joshua (Fri Feb 02 2018 - 15:55:35 CST)
Re: all-atom to coarse-grained system Rabeta Yeasmin (Fri Feb 02 2018 - 15:43:57 CST)
Re: Double-defined segid, resid for more than 9999 id's Vermaas, Joshua (Fri Feb 02 2018 - 14:26:07 CST)
Re: all-atom to coarse-grained system Victor Kwan (Fri Feb 02 2018 - 14:03:39 CST)
Double-defined segid, resid for more than 9999 id's Chun Heung Wong (Fri Feb 02 2018 - 10:17:30 CST)
Re: Calculate energy of a residue using NAMD energy Monika Madhavi (Fri Feb 02 2018 - 01:05:47 CST)
Re: Calculate energy of a residue using NAMD energy Peter Freddolino (Thu Feb 01 2018 - 22:59:57 CST)
Re: Calculate energy of a residue using NAMD energy Monika Madhavi (Thu Feb 01 2018 - 22:51:37 CST)
Re: Calculate energy of a residue using NAMD energy Peter Freddolino (Thu Feb 01 2018 - 21:59:53 CST)
Re: Calculate energy of a residue using NAMD energy Monika Madhavi (Thu Feb 01 2018 - 18:08:15 CST)
all-atom to coarse-grained system Rabeta Yeasmin (Thu Feb 01 2018 - 15:29:45 CST)
Re: trouble with colvars module Giacomo Fiorin (Thu Feb 01 2018 - 12:54:34 CST)
trouble with colvars module Artur Hermano (Thu Feb 01 2018 - 12:48:02 CST)
Re: colvars selecting frames Florian Blanc (Thu Feb 01 2018 - 10:21:18 CST)
Re: colvars selecting frames Giacomo Fiorin (Thu Feb 01 2018 - 10:03:14 CST)
Re: colvars selecting frames Stefano Guglielmo (Thu Feb 01 2018 - 06:06:41 CST)
Re: Calculate energy of a residue using NAMD energy Onur SerÃ§inoÄŸlu (Thu Feb 01 2018 - 06:06:08 CST)
[NAMD] Units of Efieldfreq The Cromicus Productions (Wed Jan 31 2018 - 23:23:16 CST)
Re: Calculate energy of a residue using NAMD energy Monika Madhavi (Wed Jan 31 2018 - 17:25:13 CST)
Re: Calculate energy of a residue using NAMD energy Peter Freddolino (Tue Jan 30 2018 - 20:51:50 CST)
colvars selecting frames Stefano Guglielmo (Tue Jan 30 2018 - 19:37:54 CST)
Re: Calculate energy of a residue using NAMD energy Monika Madhavi (Tue Jan 30 2018 - 17:41:28 CST)
Simulation of imprinting process in NAMD Abhaysinh Gaikwad (Tue Jan 30 2018 - 10:52:50 CST)
Re: Error Regarding minimization Brian Radak (Tue Jan 30 2018 - 09:51:13 CST)
Error Regarding minimization Aashish Bhatt (Tue Jan 30 2018 - 09:36:37 CST)
Re: Calculate energy of a residue using NAMD energy Brian Radak (Tue Jan 30 2018 - 09:18:44 CST)
Calculate energy of a residue using NAMD energy Monika Madhavi (Mon Jan 29 2018 - 21:22:19 CST)
Re: Question on restraint behavior when part of system decouples JÃ©rÃ´me HÃ©nin (Mon Jan 29 2018 - 16:20:22 CST)
Re: Question on restraint behavior when part of system decouples JÃ©rÃ´me HÃ©nin (Mon Jan 29 2018 - 13:52:07 CST)
Re: Question on restraint behavior when part of system decouples Randy J. Zauhar (Mon Jan 29 2018 - 13:24:45 CST)
Re: Question on restraint behavior when part of system decouples Brian Radak (Mon Jan 29 2018 - 11:19:00 CST)
Re: Calculation of Diffusion coefficient Souvik Sinha (Mon Jan 29 2018 - 11:13:55 CST)
Re: Calculation of Diffusion coefficient Giacomo Fiorin (Mon Jan 29 2018 - 10:43:27 CST)
Re: Calculation of Diffusion coefficient Souvik Sinha (Mon Jan 29 2018 - 10:35:57 CST)
Re: Stress calculation Giacomo Fiorin (Mon Jan 29 2018 - 10:17:58 CST)
Stress calculation Abhaysinh Gaikwad (Mon Jan 29 2018 - 10:04:34 CST)
Re: Calculation of Diffusion coefficient Giacomo Fiorin (Mon Jan 29 2018 - 10:02:19 CST)
Re: Question on restraint behavior when part of system decouples JÃ©rÃ´me HÃ©nin (Mon Jan 29 2018 - 09:53:51 CST)
Question on restraint behavior when part of system decouples Randy J. Zauhar (Mon Jan 29 2018 - 09:19:28 CST)
Calculation of Diffusion coefficient Souvik Sinha (Mon Jan 29 2018 - 08:01:13 CST)
Re: Replica exchange simulation with GPU Accelaration Souvik Sinha (Mon Jan 29 2018 - 05:30:39 CST)
Fwd: pressure in interfacial tension Kowsar Khajeh (Sun Jan 28 2018 - 21:18:39 CST)
Re: Stress calculation Abhaysinh Gaikwad (Sun Jan 28 2018 - 15:50:37 CST)
minimization Suresh Ghimire (Sat Jan 27 2018 - 01:29:00 CST)
Re: Replica exchange simulation with GPU Accelaration Souvik Sinha (Fri Jan 26 2018 - 23:20:14 CST)
Re: Replica exchange simulation with GPU Accelaration Jeff Comer (Fri Jan 26 2018 - 15:46:57 CST)
Re: Replica exchange simulation with GPU Accelaration Souvik Sinha (Fri Jan 26 2018 - 13:35:12 CST)
Re: Replica exchange simulation with GPU Accelaration Giacomo Fiorin (Fri Jan 26 2018 - 13:18:17 CST)
Re: Replica exchange simulation with GPU Accelaration Souvik Sinha (Fri Jan 26 2018 - 13:02:56 CST)
Re: Replica exchange simulation with GPU Accelaration Giacomo Fiorin (Fri Jan 26 2018 - 12:32:55 CST)
Re: Replica exchange simulation with GPU Accelaration Souvik Sinha (Fri Jan 26 2018 - 12:24:27 CST)
Re: Replica exchange simulation with GPU Accelaration Giacomo Fiorin (Fri Jan 26 2018 - 09:12:28 CST)
Re: Replica exchange simulation with GPU Accelaration Renfro, Michael (Thu Jan 25 2018 - 13:40:28 CST)
Re: Replica exchange simulation with GPU Accelaration Souvik Sinha (Thu Jan 25 2018 - 12:59:26 CST)
Re: Replica exchange simulation with GPU Accelaration Giacomo Fiorin (Thu Jan 25 2018 - 08:22:24 CST)
Replica exchange simulation with GPU Accelaration Souvik Sinha (Thu Jan 25 2018 - 03:02:15 CST)
Q=9E=D1=82=D0=B2=D0=B5=D1=82:=20Re:=20=20none?= quilibrium SMD with fixed atoms Ekaterina Sobakinskaja (Wed Jan 24 2018 - 13:58:29 CST)
Re: nonequilibrium SMD with fixed atoms Giacomo Fiorin (Wed Jan 24 2018 - 10:11:18 CST)
Re: Missing Parameters For H3O+ Ahmad Kiani (Wed Jan 24 2018 - 09:27:28 CST)
nonequilibrium SMD with fixed atoms Ekaterina Sobakinskaja (Wed Jan 24 2018 - 09:27:28 CST)
Re: Missing Parameters For H3O+ Brian Radak (Wed Jan 24 2018 - 09:05:36 CST)
Re: Missing Parameters For H3O+ Giacomo Fiorin (Wed Jan 24 2018 - 08:41:47 CST)
Re: Missing Parameters For H3O+ Victor Kwan (Tue Jan 23 2018 - 22:16:11 CST)
Re: Missing Parameters For H3O+ Victor Kwan (Tue Jan 23 2018 - 22:03:20 CST)
Missing Parameters For H3O+ Ahmad Kiani (Tue Jan 23 2018 - 12:13:00 CST)
Re: Vectors and indexing in VMD Chang Sun (Tue Jan 23 2018 - 10:35:35 CST)
Vectors and indexing in VMD Chun Heung Wong (Tue Jan 23 2018 - 06:16:00 CST)
Re: Trouble with NAMD Win64-CUDA 2.12 on my new PC Florian Blanc (Mon Jan 22 2018 - 11:29:45 CST)
Trouble with NAMD Win64-CUDA 2.12 on my new PC Yu Zhou (Mon Jan 22 2018 - 11:24:26 CST)
Re: Ways to find water molecules passing through the water channel in lipid bilayer Vermaas, Joshua (Fri Jan 19 2018 - 13:37:56 CST)
Re: Ways to find water molecules passing through the water channel in lipid bilayer Rabeta Yeasmin (Fri Jan 19 2018 - 13:13:31 CST)
Re: Ways to find water molecules passing through the water channel in lipid bilayer Giacomo Fiorin (Thu Jan 18 2018 - 18:54:48 CST)
Re: Ways to find water molecules passing through the water channel in lipid bilayer Bassam Haddad (Thu Jan 18 2018 - 18:46:46 CST)
Re: Ways to find water molecules passing through the water channel in lipid bilayer Rabeta Yeasmin (Thu Jan 18 2018 - 18:43:06 CST)
Re: Ways to find water molecules passing through the water channel in lipid bilayer Giacomo Fiorin (Thu Jan 18 2018 - 18:38:33 CST)
Tilting angle of lipid calculation Rabeta Yeasmin (Thu Jan 18 2018 - 18:29:44 CST)
Ways to find water molecules passing through the water channel in lipid bilayer Rabeta Yeasmin (Thu Jan 18 2018 - 18:19:29 CST)
Re: Hamiltonian Replica Exchange MD in NAMD JC Gumbart (Thu Jan 18 2018 - 18:02:37 CST)
Re: Hamiltonian Replica Exchange MD in NAMD Vermaas, Joshua (Thu Jan 18 2018 - 16:14:04 CST)
Hamiltonian Replica Exchange MD in NAMD Youngwoo Woo (Thu Jan 18 2018 - 16:01:28 CST)
Re: acceptor Giacomo Fiorin (Thu Jan 18 2018 - 06:50:07 CST)
Re: UNABLE TO FIND ANGLE PARAMETERS FOR CD OH1 CD (ATOMS 282 284 282) Victor Kwan (Wed Jan 17 2018 - 11:59:44 CST)
Re: Stress calculation Giacomo Fiorin (Wed Jan 17 2018 - 10:42:31 CST)
Re: acceptor Giacomo Fiorin (Wed Jan 17 2018 - 10:20:34 CST)
acceptor Suresh Ghimire (Wed Jan 17 2018 - 00:02:10 CST)
accepter Suresh Ghimire (Tue Jan 16 2018 - 23:51:20 CST)
Re: UNABLE TO FIND ANGLE PARAMETERS FOR CD OH1 CD (ATOMS 282 284 282) Vermaas, Joshua (Tue Jan 16 2018 - 13:54:29 CST)
UNABLE TO FIND ANGLE PARAMETERS FOR CD OH1 CD (ATOMS 282 284 282) Ahmad Kiani (Tue Jan 16 2018 - 11:13:20 CST)
Stress calculation Abhaysinh Gaikwad (Tue Jan 16 2018 - 09:03:15 CST)
Re: Different resid in pdb fie but showing same molecule in VMD Rabeta Yeasmin (Mon Jan 15 2018 - 01:57:54 CST)
(no subject) Suresh Ghimire (Sun Jan 14 2018 - 07:31:05 CST)
Re: Different resid in pdb fie but showing same molecule in VMD Chitrak Gupta (Fri Jan 12 2018 - 19:00:01 CST)
Different resid in pdb fie but showing same molecule in VMD Rabeta Yeasmin (Fri Jan 12 2018 - 17:42:14 CST)
Re: reinitatoms Brian Radak (Fri Jan 12 2018 - 14:20:14 CST)
Re: SMD: Combined Constant Velocity and Constant Force method Giacomo Fiorin (Thu Jan 11 2018 - 15:56:28 CST)
SMD: Combined Constant Velocity and Constant Force method Keshab Thapa (Thu Jan 11 2018 - 15:51:18 CST)
Re: reinitatoms Laura Joana (Thu Jan 11 2018 - 10:36:31 CST)
reinitatoms Laura Joana (Thu Jan 11 2018 - 08:26:28 CST)
Pressure ? High values ; Pressavg Gpressavg ? value of first step of restart very different from the last of the previous MD Charline FAGNEN (Tue Jan 09 2018 - 10:09:16 CST)
Re: Setting up GPU workstation advice Jeff Comer (Mon Jan 08 2018 - 10:04:52 CST)
Re: Setting up GPU workstation advice horacio poblete (Mon Jan 08 2018 - 07:17:52 CST)
Re: Haohao Fu (Sun Jan 07 2018 - 21:02:01 CST)
Setting up GPU workstation advice Lewis Martin (Sun Jan 07 2018 - 20:28:49 CST)
(no subject) Suresh Ghimire (Sun Jan 07 2018 - 04:09:05 CST)
Re: Roshan Shrestha (Sat Jan 06 2018 - 09:56:26 CST)
(no subject) Suresh Ghimire (Sat Jan 06 2018 - 09:46:20 CST)
having problem with disulfide bond Shahee Islam (Thu Jan 04 2018 - 05:48:38 CST)
Re: Having problem with restarting colvar distance, Aliasghar Alizadeh-Mojarad (Wed Jan 03 2018 - 13:44:19 CST)
metadynamics reaction coordinate Rabeta Yeasmin (Wed Jan 03 2018 - 11:42:57 CST)
Re: Having problem with restarting colvar distance, Giacomo Fiorin (Wed Jan 03 2018 - 11:02:00 CST)
Re: Having problem with restarting colvar distance, Aliasghar Alizadeh-Mojarad (Wed Jan 03 2018 - 10:35:52 CST)
(no subject) Suresh Ghimire (Mon Jan 01 2018 - 09:14:36 CST)

Last message date: Mon Dec 30 2019 - 20:12:28 CST
Archived on: Tue Dec 31 2019 - 23:21:04 CST

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