NAMD-L: By Thread

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NAMD-L: By Thread

By Thread

3174 messages sorted by: [ author ] [ date ] [ subject ] [ attachment ]
About this archive

Starting: Wed Jan 01 2014 - 05:18:45 CST
Ending: Tue Dec 29 2015 - 07:12:19 CST

Energy decomposition analyse in NAMD sunyzero (Mon Dec 28 2015 - 20:23:28 CST)
Restraints on the outer solutes Diksha Dubey (Mon Dec 28 2015 - 03:39:00 CST)
- Re: Restraints on the outer solutes Vibhor Agrawal (Mon Dec 28 2015 - 03:50:57 CST)
mail reg parameters Vidhya Sankar (Fri Dec 25 2015 - 20:51:57 CST)
- Re: mail reg parameters sena (Fri Dec 25 2015 - 22:29:17 CST)
DIDN'T FIND vdW PARAMETER FOR ATOM TYPE SG3O1 Srijita Paul (Fri Dec 25 2015 - 00:41:47 CST)
SMD with PBC Mahdi Tavakol (Thu Dec 24 2015 - 00:22:36 CST)
Add ions/molecules different from Autoionize defaults Ardavan Mehdizadeh (Thu Dec 24 2015 - 07:37:01 CST)
- Re: Add ions/molecules different from Autoionize defaults Peter Freddolino (Thu Dec 24 2015 - 08:45:43 CST)
  - Re: Add ions/molecules different from Autoionize defaults amin_at_imtech.res.in (Fri Dec 25 2015 - 07:16:46 CST)
  - Re: Add ions/molecules different from Autoionize defaults Ardavan Mehdizadeh (Fri Dec 25 2015 - 12:28:43 CST)
Add ions/molecules different from Autoionize defaults Ardavan Mehdizadeh (Wed Dec 23 2015 - 12:05:36 CST)
- Re: Add ions/molecules different from Autoionize defaults Ardavan Mehdizadeh (Thu Dec 24 2015 - 07:37:39 CST)
LangevinDamping Coefficient for MARTINI Mahdi Tavakol (Wed Dec 23 2015 - 05:33:48 CST)
NAMD 2.11 released Jim Phillips (Tue Dec 22 2015 - 10:38:50 CST)
- Re: NAMD 2.11 released Branko (Tue Dec 22 2015 - 16:19:37 CST)
  - Re: NAMD 2.11 released Jim Phillips (Tue Dec 22 2015 - 21:37:31 CST)
The script of Umbrella sampling sunyzero (Tue Dec 22 2015 - 03:33:13 CST)
- Re: The script of Umbrella sampling JC Gumbart (Fri Dec 25 2015 - 12:49:51 CST)
(no subject) Srijita Paul (Tue Dec 22 2015 - 00:06:49 CST)
OpenGL Display Window, "Key 2", SMD with NAMD Zeinab Emami (Sun Dec 20 2015 - 11:57:52 CST)
how to get the restart files from the dcd file? Azadeh Alavi (Sun Dec 20 2015 - 03:02:36 CST)
- Re: how to get the restart files from the dcd file? Jeff Comer (Sun Dec 20 2015 - 12:06:17 CST)
  - Re: how to get the restart files from the dcd file? Jeff Comer (Sun Dec 20 2015 - 12:46:16 CST)
    - Re: how to get the restart files from the dcd file? Azadeh Alavi (Sun Dec 20 2015 - 14:30:07 CST)
  - Re: how to get the restart files from the dcd file? Azadeh Alavi (Mon Dec 21 2015 - 07:10:47 CST)
MD simulation of Linear Molecules (like 2-butyne£© Ô¬Ð¡¾§ (Fri Dec 18 2015 - 20:26:26 CST)
- Re: MD simulation of Linear Molecules (like 2-butyne£© Jim Phillips (Sat Dec 19 2015 - 21:53:01 CST)
  - Re: Re: MD simulation of Linear Molecules (like 2-butyne£© Ô¬Ð¡¾§ (Mon Dec 21 2015 - 20:30:09 CST)
RE: SMP NAMD reports threads greater than physical cores, even when distributed to other nodes Jim Phillips (Fri Dec 18 2015 - 09:38:15 CST)
- RE: SMP NAMD reports threads greater than physical cores, even when distributed to other nodes Tom Coles (Fri Dec 18 2015 - 15:16:01 CST)
  - RE: SMP NAMD reports threads greater than physical cores, even when distributed to other nodes Jim Phillips (Sat Dec 19 2015 - 21:39:50 CST)
SMP NAMD reports threads greater than physical cores, even when distributed to other nodes Tom Coles (Thu Dec 17 2015 - 10:26:20 CST)
ERROR in CUDA run Lara rajam (Thu Dec 17 2015 - 08:50:49 CST)
- AW: ERROR in CUDA run Norman Geist (Thu Dec 17 2015 - 09:24:20 CST)
- Re: ERROR in CUDA run Jim Phillips (Thu Dec 17 2015 - 19:50:54 CST)
"implausibly old time stamp" for charm++ 6.7 in CVS Brian Radak (Wed Dec 16 2015 - 11:42:29 CST)
- Re: "implausibly old time stamp" for charm++ 6.7 in CVS Jim Phillips (Mon Dec 21 2015 - 10:04:11 CST)
Number of pdb and psf atoms are not the same! Francesco Pietra (Wed Dec 16 2015 - 09:23:41 CST)
- Re: vmd-l: Number of pdb and psf atoms are not the same! Ashar Malik (Wed Dec 16 2015 - 09:57:47 CST)
  - Re: vmd-l: Number of pdb and psf atoms are not the same! Francesco Pietra (Wed Dec 16 2015 - 10:14:12 CST)
RATTLE Error During Minimization of Charmm Gui Generated Bilayer begÃ¼m alaybeyoÄŸlu (Tue Dec 15 2015 - 10:27:48 CST)
- Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer Chitrak Gupta (Tue Dec 15 2015 - 12:46:36 CST)
  - Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer begÃ¼m alaybeyoÄŸlu (Wed Dec 16 2015 - 03:46:10 CST)
  - Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer Jim Phillips (Thu Dec 17 2015 - 19:49:32 CST)
    - Re: RATTLE Error During Minimization of Charmm Gui Generated Bilayer Chitrak Gupta (Fri Dec 18 2015 - 09:08:27 CST)
free energy changes via FEP method Haleh a (Tue Dec 15 2015 - 09:59:10 CST)
- Re: free energy changes via FEP method Brian Radak (Wed Dec 16 2015 - 12:15:10 CST)
  - Re: free energy changes via FEP method Gianluca Interlandi (Wed Dec 16 2015 - 12:49:26 CST)
    - Re: free energy changes via FEP method Haleh a (Thu Dec 17 2015 - 05:42:15 CST)
Viscosity Calculation using EMD Gaurab Sarkar (Mon Dec 14 2015 - 13:22:02 CST)
Usage of velDCDfile and forceDCDfile keywords in viscosity calculations Debashis Kundu (Mon Dec 14 2015 - 00:34:56 CST)
OutputAccumulatedWork...where's the output? Bryan Roessler (Sun Dec 13 2015 - 19:36:26 CST)
- Re: OutputAccumulatedWork...where's the output? Giacomo Fiorin (Mon Dec 14 2015 - 10:55:36 CST)
  - Re: OutputAccumulatedWork...where's the output? Bryan Roessler (Mon Dec 14 2015 - 12:41:08 CST)
    - Re: OutputAccumulatedWork...where's the output? Giacomo Fiorin (Mon Dec 14 2015 - 13:32:17 CST)
VMD-NAMD and PDB element column Francesco Pietra (Sat Dec 12 2015 - 09:09:55 CST)
- Re: VMD-NAMD and PDB element column Jim Phillips (Sun Dec 13 2015 - 12:17:57 CST)
  - Re: vmd-l: Re: VMD-NAMD and PDB element column Francesco Pietra (Sun Dec 13 2015 - 13:39:11 CST)
Problems with GLUP and ASPP with CHARMM36 Francesco Pietra (Fri Dec 11 2015 - 05:07:03 CST)
- Re: Problems with GLUP and ASPP with CHARMM36 Josh Vermaas (Fri Dec 11 2015 - 08:45:00 CST)
  - Re: Problems with GLUP and ASPP with CHARMM36 Francesco Pietra (Fri Dec 11 2015 - 09:21:34 CST)
    - Re: Problems with GLUP and ASPP with CHARMM36 Josh Vermaas (Fri Dec 11 2015 - 09:25:11 CST)
  - Re: Problems with GLUP and ASPP with CHARMM36 Francesco Pietra (Fri Dec 11 2015 - 09:35:48 CST)
PRES and water-ions issues with charmm36 Francesco Pietra (Thu Dec 10 2015 - 15:30:14 CST)
- Re: vmd-l: PRES and water-ions issues with charmm36 Brian Radak (Thu Dec 10 2015 - 15:58:49 CST)
extendedLagrangian for non-scalar colvar Jerome Karp (Thu Dec 10 2015 - 10:45:27 CST)
- Re: extendedLagrangian for non-scalar colvar JÃ©rÃ´me HÃ©nin (Thu Dec 10 2015 - 11:18:39 CST)
  - Re: extendedLagrangian for non-scalar colvar Jerome Karp (Thu Dec 10 2015 - 12:05:51 CST)
energy output Deng, Jinxia (Nancy) (Wed Dec 09 2015 - 11:39:14 CST)
- Re: energy output Chitrak Gupta (Wed Dec 09 2015 - 11:47:57 CST)
- Re: energy output Branko (Wed Dec 09 2015 - 11:51:45 CST)
- Re: energy output Jeffrey Potoff (Wed Dec 09 2015 - 11:56:45 CST)
  - RE: energy output Deng, Jinxia (Nancy) (Wed Dec 09 2015 - 13:12:11 CST)
NAMD on TACC (Darter) Chitrak Gupta (Tue Dec 08 2015 - 18:16:29 CST)
- Re: NAMD on TACC (Darter) Jim Phillips (Tue Dec 08 2015 - 22:15:15 CST)
  - Re: NAMD on TACC (Darter) Chitrak Gupta (Tue Dec 08 2015 - 22:19:12 CST)
buffer overflow with long file paths in psfgen in NAMD 2.11b2? Brian Radak (Tue Dec 08 2015 - 15:54:28 CST)
- Re: buffer overflow with long file paths in psfgen in NAMD 2.11b2? Jim Phillips (Tue Dec 08 2015 - 16:41:22 CST)
anionic cysteine Francesco Pietra (Tue Dec 08 2015 - 08:50:19 CST)
- Re: anionic cysteine Tristan Croll (Tue Dec 08 2015 - 22:00:12 CST)
  - Re: anionic cysteine Francesco Pietra (Wed Dec 09 2015 - 04:13:54 CST)
    - Re: anionic cysteine Tristan Croll (Wed Dec 09 2015 - 04:23:03 CST)
Determining the PMF with Adaptive Biasing Forces sunyzero (Mon Dec 07 2015 - 23:48:55 CST)
- Re: Determining the PMF with Adaptive Biasing Forces Souvik Sinha (Tue Dec 08 2015 - 01:42:34 CST)
  - Re: Determining the PMF with Adaptive Biasing Forces JÃ©rÃ´me HÃ©nin (Tue Dec 08 2015 - 09:09:58 CST)
    - Re:Re: Determining the PMF with Adaptive Biasing Forces sunyzero (Tue Dec 08 2015 - 22:00:19 CST)
Determining the PMF with Adaptive Biasing Forces sunyzero (Mon Dec 07 2015 - 20:02:35 CST)
multiple output .dcd files?? Deng, Jinxia (Nancy) (Mon Dec 07 2015 - 14:56:53 CST)
- Re: multiple output .dcd files?? Jim Phillips (Mon Dec 07 2015 - 16:43:12 CST)
  - RE: multiple output .dcd files?? Deng, Jinxia (Nancy) (Tue Dec 08 2015 - 08:43:02 CST)
NAMD 2.11b2 released Jim Phillips (Sun Dec 06 2015 - 22:01:09 CST)
namd2.22b CUDA Phi Francesco Pietra (Sat Dec 05 2015 - 01:06:49 CST)
- Re: namd2.22b CUDA Phi Jim Phillips (Sat Dec 05 2015 - 08:50:57 CST)
modify input file for production phase MD Deng, Jinxia (Nancy) (Fri Dec 04 2015 - 11:31:26 CST)
- Re: modify input file for production phase MD Branko (Fri Dec 04 2015 - 11:50:53 CST)
Overflow in LJcorrection? Brian Radak (Thu Dec 03 2015 - 15:45:38 CST)
- Re: Overflow in LJcorrection? Jason Swails (Thu Dec 03 2015 - 15:55:30 CST)
- Re: Overflow in LJcorrection? Peter Freddolino (Thu Dec 03 2015 - 15:55:49 CST)
  - Re: Overflow in LJcorrection? Brian Radak (Thu Dec 03 2015 - 15:59:27 CST)
  - Re: Overflow in LJcorrection? Jason Swails (Thu Dec 03 2015 - 16:04:28 CST)
NAMD 2.11b1 multicore CUDA: Incorrect number of exclusions Jeff Comer (Thu Dec 03 2015 - 14:20:42 CST)
- Re: NAMD 2.11b1 multicore CUDA: Incorrect number of exclusions Jim Phillips (Fri Dec 04 2015 - 16:52:30 CST)
Re: concerning paratools Mayne, Christopher G (Thu Dec 03 2015 - 14:11:52 CST)
error when use Charmm_Gui prepared *.inp for NAMD Deng, Jinxia (Nancy) (Thu Dec 03 2015 - 08:37:14 CST)
- Re: error when use Charmm_Gui prepared *.inp for NAMD Chitrak Gupta (Thu Dec 03 2015 - 08:49:59 CST)
  - RE: error when use Charmm_Gui prepared *.inp for NAMD Deng, Jinxia (Nancy) (Thu Dec 03 2015 - 09:52:20 CST)
- Re: error when use Charmm_Gui prepared *.inp for NAMD Josh Vermaas (Thu Dec 03 2015 - 08:50:36 CST)
- Re: error when use Charmm_Gui prepared *.inp for NAMD Jeffrey Potoff (Thu Dec 03 2015 - 08:44:53 CST)
concerning paratools luca belmonte (Thu Dec 03 2015 - 04:36:04 CST)
fructose 1,6 bisphosphate forcefield parameters. Dhiraj Srivastava (Wed Dec 02 2015 - 00:06:45 CST)
accelerated MD new variant Vlad Cojocaru (Sun Nov 29 2015 - 03:53:20 CST)
- Re: accelerated MD new variant Brian Radak (Mon Nov 30 2015 - 09:48:36 CST)
  - Re: accelerated MD new variant Vlad Cojocaru (Mon Nov 30 2015 - 10:00:35 CST)
Fwd: TIP4P and CHARMM27 Francesco Pietra (Fri Nov 27 2015 - 09:17:35 CST)
- Re: Fwd: TIP4P and CHARMM27 Peter Freddolino (Fri Nov 27 2015 - 09:41:00 CST)
  - Re: Fwd: TIP4P and CHARMM27 Francesco Pietra (Fri Nov 27 2015 - 10:18:28 CST)
- Re: Fwd: TIP4P and CHARMM27 Jim Phillips (Mon Nov 30 2015 - 16:21:44 CST)
  - Re: Fwd: TIP4P and CHARMM27 Francesco Pietra (Tue Dec 01 2015 - 03:22:31 CST)
DOF during alchemical simulations Brian Radak (Wed Nov 25 2015 - 10:31:11 CST)
- Re: DOF during alchemical simulations JÃ©rÃ´me HÃ©nin (Thu Nov 26 2015 - 12:00:01 CST)
  - Re: DOF during alchemical simulations Aron Broom (Thu Nov 26 2015 - 12:28:27 CST)
Q=B4=D7=D4"ZOU_Changling"_<zoucl@ihep.ac.cn>=B5=C4=D3=CA=BC=FE?= ZOU Changling (Wed Nov 25 2015 - 06:39:26 CST)
- Re: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓÊ¼þ Abhishek TYAGI (Wed Nov 25 2015 - 07:03:45 CST)
recommendations for a fast multicore workstation Jeff Comer (Tue Nov 24 2015 - 11:56:54 CST)
Re: how does NAMD calculate intramolecular electrostatic interactions between Drude pairs? Ana Celia Vila Verde (Mon Nov 23 2015 - 09:27:00 CST)
- Re: how does NAMD calculate intramolecular electrostatic interactions between Drude pairs? Ana Celia Vila Verde (Thu Nov 26 2015 - 01:13:38 CST)
Which namd to use Maxime Boissonneault (Fri Nov 20 2015 - 07:29:45 CST)
- Re: Which namd to use Jim Phillips (Fri Nov 20 2015 - 08:02:36 CST)
  - Re: Which namd to use Maxime Boissonneault (Fri Nov 20 2015 - 08:13:58 CST)
    - Re: Which namd to use Jim Phillips (Fri Nov 20 2015 - 11:11:30 CST)
query for system size in pmf calculation Atanu Maity (Fri Nov 20 2015 - 05:24:47 CST)
- Re: query for system size in pmf calculation Giacomo Fiorin (Fri Nov 20 2015 - 08:52:35 CST)
Crazy rigid water molecules Brian Radak (Thu Nov 19 2015 - 15:40:55 CST)
Changing Boundary conditions from PBC to non-periodic Mahdi Tavakol (Thu Nov 19 2015 - 12:30:23 CST)
- Re: Changing Boundary conditions from PBC to non-periodic Gianluca Interlandi (Thu Nov 19 2015 - 14:30:16 CST)
  - AW: Changing Boundary conditions from PBC to non-periodic Norman Geist (Fri Nov 20 2015 - 01:52:26 CST)
NAMD2.11 source code not compiling Madhulika Gupta (Wed Nov 18 2015 - 02:47:38 CST)
- Re: NAMD2.11 source code not compiling Jim Phillips (Wed Nov 18 2015 - 09:21:13 CST)
  - Re: NAMD2.11 source code not compiling Madhulika Gupta (Wed Nov 18 2015 - 10:31:55 CST)
  - Re: NAMD2.11 source code not compiling Madhulika Gupta (Fri Nov 20 2015 - 01:20:05 CST)
Fw: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓÊ¼þ ZOU Changling (Wed Nov 18 2015 - 00:26:54 CST)
- Fw: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓÊ¼þ ZOU Changling (Wed Nov 18 2015 - 02:43:26 CST)
  - Fw: Fw: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓÊ¼þ ZOU Changling (Wed Nov 18 2015 - 02:40:15 CST)
- Re: Fw: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓÊ¼þ Abhishek TYAGI (Wed Nov 18 2015 - 09:45:45 CST)
  - Re: Re: Fw: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓÊ¼þ ZOU Changling (Wed Nov 18 2015 - 19:34:42 CST)
    - Re: Re: Fw: À´×Ô"ZOU Changling" <zoucl@ihep.ac.cn>µÄÓÊ¼þ Abhishek TYAGI (Wed Nov 18 2015 - 20:12:47 CST)
    - Re: Re: Fw: æ¥è‡ª"ZOU Changling" <zoucl@ihep.ac.cn>çš„é‚®ä»¶ Axel Kohlmeyer (Wed Nov 18 2015 - 20:15:49 CST)
Q=B4=D7=D4"ZOU_Changling"_<zoucl@ihep.ac.cn>=B5=C4=D3=CA=BC=FE?= ZOU Changling (Wed Nov 18 2015 - 00:25:35 CST)
Can't start SMP NAMD - Problem clearly is in front of the monitor Vogel, Alexander (Tue Nov 17 2015 - 03:18:05 CST)
- Re: Can't start SMP NAMD - Problem clearly is in front of the monitor Jim Phillips (Tue Nov 17 2015 - 12:45:51 CST)
ABF calculations - reaction coordinate Mohan maruthi sena (Mon Nov 16 2015 - 19:15:15 CST)
- Re: ABF calculations - reaction coordinate Giacomo Fiorin (Mon Nov 16 2015 - 20:30:56 CST)
Free energy profiles in ABF tutorial Haleh a (Mon Nov 16 2015 - 06:35:30 CST)
- Re: Free energy profiles in ABF tutorial Giacomo Fiorin (Mon Nov 16 2015 - 07:52:31 CST)
Bubble in water during membrane simulations Kevin C Chan (Mon Nov 16 2015 - 02:12:29 CST)
- Re: Bubble in water during membrane simulations Giacomo Fiorin (Mon Nov 16 2015 - 09:48:42 CST)
  - Re: Bubble in water during membrane simulations Kevin Chan (Mon Nov 16 2015 - 10:41:21 CST)
time per step during GPU-accelerated Implicit Solvent calculations Thomas Albers (Sun Nov 15 2015 - 19:11:26 CST)
- AW: time per step during GPU-accelerated Implicit Solvent calculations Norman Geist (Mon Nov 16 2015 - 01:52:00 CST)
  - Re: AW: time per step during GPU-accelerated Implicit Solvent calculations Jim Phillips (Mon Nov 16 2015 - 08:55:26 CST)
  - Re: AW: time per step during GPU-accelerated Implicit Solvent calculations Thomas Albers (Wed Nov 18 2015 - 08:38:07 CST)
NAMD 2.11 CUDA forces IBverbs Norman Geist (Fri Nov 13 2015 - 06:00:18 CST)
- Re: NAMD 2.11 CUDA forces IBverbs Jim Phillips (Fri Nov 13 2015 - 08:31:50 CST)
FATAL ERROR: Unable to access config file ubq_ws_eq.log Hugo Siles (Thu Nov 12 2015 - 16:40:41 CST)
- Re: FATAL ERROR: Unable to access config file ubq_ws_eq.log Jim Phillips (Thu Nov 12 2015 - 22:45:32 CST)
FEP using separated topologies David Huggins (Thu Nov 12 2015 - 07:46:54 CST)
- Re: FEP using separated topologies JÃ©rÃ´me HÃ©nin (Thu Nov 12 2015 - 08:48:12 CST)
Would it be possible to continue a simulation from any snapshot of a trajectory? sunyeping (Thu Nov 12 2015 - 02:45:51 CST)
- Re: Would it be possible to continue a simulation from any snapshot of a trajectory? Felipe Merino (Thu Nov 12 2015 - 03:33:05 CST)
  - Re: Would it be possible to continue a simulation from any snapshot of a trajectory? sunyeping (Thu Nov 12 2015 - 20:57:20 CST)
Van der Waals and Electrostatic Forces - CUDA Kostas Malavazos (Tue Nov 10 2015 - 11:11:37 CST)
NAMD 2.11b1 released Jim Phillips (Tue Nov 10 2015 - 09:39:44 CST)
- Re: NAMD 2.11b1 released Tien Huynh (Tue Nov 10 2015 - 11:10:25 CST)
  - Re: NAMD 2.11b1 released sunyeping (Thu Nov 12 2015 - 02:39:43 CST)
  - Re: NAMD 2.11b1 released Jim Phillips (Thu Nov 12 2015 - 11:15:27 CST)
    - Re: NAMD 2.11b1 released Tien Huynh (Thu Nov 12 2015 - 11:24:00 CST)
- Re: NAMD 2.11b1 released Jeff Comer (Tue Nov 10 2015 - 13:18:06 CST)
- Re: NAMD 2.11b1 released Tristan Croll (Wed Nov 11 2015 - 20:11:00 CST)
On-the-fly modification of tclforces script? Tristan Croll (Tue Nov 10 2015 - 03:01:19 CST)
- AW: On-the-fly modification of tclforces script? Norman Geist (Tue Nov 10 2015 - 04:18:02 CST)
  - Re: On-the-fly modification of tclforces script? Tristan Croll (Tue Nov 10 2015 - 04:27:19 CST)
- Re: On-the-fly modification of tclforces script? Jim Phillips (Tue Nov 10 2015 - 09:53:42 CST)
  - Re: On-the-fly modification of tclforces script? Tristan Croll (Tue Nov 10 2015 - 16:03:38 CST)
Fw: vmd-l: what is difference between "TOTAL", â€œTOTAL2" and "POTENTIAL" in the VMD plugin NAMD Plot? å™ä¸šå¹³ (Mon Nov 09 2015 - 06:49:42 CST)
Re: OPLSAA to CHARMM Francesco Pietra (Fri Nov 06 2015 - 00:59:02 CST)
error reading colvars.conf in REUS Chitrak Gupta (Thu Nov 05 2015 - 16:45:48 CST)
- Re: error reading colvars.conf in REUS Giacomo Fiorin (Fri Nov 06 2015 - 14:41:42 CST)
  - Re: error reading colvars.conf in REUS Chitrak Gupta (Tue Nov 10 2015 - 20:18:11 CST)
    - Re: error reading colvars.conf in REUS Giacomo Fiorin (Wed Nov 11 2015 - 11:00:21 CST)
    - Re: error reading colvars.conf in REUS Chitrak Gupta (Mon Nov 16 2015 - 08:42:08 CST)
OPLSAA to CHARMM Francesco Pietra (Thu Nov 05 2015 - 10:21:42 CST)
pdb files to dcd Amitkumar Majhi (Tue Nov 03 2015 - 14:33:21 CST)
- Re: pdb files to dcd Josh Vermaas (Tue Nov 03 2015 - 14:40:53 CST)
Topology and parameters for Sodium dodecanoate Sadegh Faramarzi Ganjabad (Tue Nov 03 2015 - 11:21:45 CST)
- Re: Topology and parameters for Sodium dodecanoate AndrÃ© Farias de Moura (Tue Nov 03 2015 - 12:57:34 CST)
  - Re: Topology and parameters for Sodium dodecanoate Mayne, Christopher G (Wed Nov 04 2015 - 08:05:46 CST)
Multiple NAMD calculations on windows Mai Aamer (Mon Nov 02 2015 - 16:40:06 CST)
about deca alanine tutorial setup Jessen Lucas (Mon Nov 02 2015 - 15:22:16 CST)
- Re: about deca alanine tutorial setup Ajasja LjubetiÄ (Mon Nov 02 2015 - 16:14:28 CST)
  - Fwd: Re: about deca alanine tutorial setup Branko (Mon Nov 02 2015 - 16:26:57 CST)
16 total processes killed (some possibly by mpirun during cleanup) Shalton Evans (Mon Nov 02 2015 - 14:34:13 CST)
- AW: 16 total processes killed (some possibly by mpirun during cleanup) Norman Geist (Tue Nov 03 2015 - 00:25:15 CST)
How occupancy relates to force in SMD daneshkaftroody_v_at_mech.sharif.ir (Mon Nov 02 2015 - 10:41:11 CST)
substrate and membrane protein LucÃa DÃaz (Mon Nov 02 2015 - 08:03:28 CST)
ABF error on NAMD 2.10 Haleh a (Mon Nov 02 2015 - 05:55:59 CST)
- Re: ABF error on NAMD 2.10 JÃ©rÃ´me HÃ©nin (Mon Nov 02 2015 - 07:47:25 CST)
- Re: ABF error on NAMD 2.10 Giacomo Fiorin (Mon Nov 02 2015 - 07:49:46 CST)
  - Re: ABF error on NAMD 2.10 Haleh a (Mon Nov 02 2015 - 08:45:29 CST)
    - Re: ABF error on NAMD 2.10 Giacomo Fiorin (Mon Nov 02 2015 - 08:51:52 CST)
Weird psfgen bug? Tristan Croll (Fri Oct 30 2015 - 03:22:06 CDT)
Problem with tcl intepreter Bryan Roessler (Thu Oct 29 2015 - 19:24:53 CDT)
- Re: Problem with tcl intepreter Josh Vermaas (Thu Oct 29 2015 - 19:45:12 CDT)
  - Re: Problem with tcl intepreter Bryan Roessler (Thu Oct 29 2015 - 20:06:58 CDT)
    - Re: Problem with tcl intepreter Belkin, Maxim (Tue Nov 03 2015 - 10:53:53 CST)
- Re: Problem with tcl intepreter Axel Kohlmeyer (Thu Oct 29 2015 - 19:54:34 CDT)
- Re: Problem with tcl intepreter Bryan Roessler (Thu Oct 29 2015 - 20:00:31 CDT)
Including two parameters for protein-ligand simulation Nikhil Maroli (Wed Oct 28 2015 - 01:52:30 CDT)
- Re: Including two parameters for protein-ligand simulation Abhishek TYAGI (Wed Oct 28 2015 - 01:59:21 CDT)
  - Re: vmd-l: Re: Including two parameters for protein-ligand simulation Payal Chatterjee (Wed Oct 28 2015 - 03:08:16 CDT)
- Re: vmd-l: Including two parameters for protein-ligand simulation Sourav Ray (Wed Oct 28 2015 - 02:20:04 CDT)
namd 2.10 crashes when using more than 1 CPU for FEP simulation Tien Huynh (Tue Oct 27 2015 - 21:58:14 CDT)
Biasing potential of a Metadynamics Simulation Fidan Sumbul (Tue Oct 27 2015 - 13:05:02 CDT)
- Re: Biasing potential of a Metadynamics Simulation Giacomo Fiorin (Tue Oct 27 2015 - 13:14:06 CDT)
  - Re: Biasing potential of a Metadynamics Simulation Fidan Sumbul (Tue Oct 27 2015 - 14:38:16 CDT)
    - Re: Biasing potential of a Metadynamics Simulation Giacomo Fiorin (Tue Oct 27 2015 - 15:55:13 CDT)
ANGLE PARAMETERS FOR NH3 HC NH3 Francesco Pietra (Tue Oct 27 2015 - 11:12:20 CDT)
- Fwd: ANGLE PARAMETERS FOR NH3 HC NH3 Francesco Pietra (Tue Oct 27 2015 - 11:19:48 CDT)
  - Re: Fwd: ANGLE PARAMETERS FOR NH3 HC NH3 Josh Vermaas (Tue Oct 27 2015 - 11:24:47 CDT)
    - Re: Fwd: ANGLE PARAMETERS FOR NH3 HC NH3 Francesco Pietra (Tue Oct 27 2015 - 13:33:59 CDT)
    - RE: Fwd: ANGLE PARAMETERS FOR NH3 HC NH3 Tristan Croll (Wed Oct 28 2015 - 20:36:08 CDT)
Lennard-Jones and Electrostatic Forces and Energies Kostas Malavazos (Mon Oct 26 2015 - 13:54:28 CDT)
- Re: Lennard-Jones and Electrostatic Forces and Energies Brian Radak (Tue Oct 27 2015 - 08:50:27 CDT)
replica exchange module Jessen Lucas (Mon Oct 26 2015 - 01:29:43 CDT)
- AW: replica exchange module Norman Geist (Mon Oct 26 2015 - 02:11:47 CDT)
  - Re: replica exchange module Jessen Lucas (Mon Oct 26 2015 - 02:25:49 CDT)
constraint failure in Rattle algorithm for atom 54134 Life Sciences Inc (Sun Oct 25 2015 - 19:42:57 CDT)
- Re: constraint failure in Rattle algorithm for atom 54134 Chitrak Gupta (Mon Oct 26 2015 - 08:31:44 CDT)
  - Re: constraint failure in Rattle algorithm for atom 54134 Chitrak Gupta (Mon Oct 26 2015 - 13:01:16 CDT)
    - Re: constraint failure in Rattle algorithm for atom 54134 Life Sciences Inc (Mon Oct 26 2015 - 13:37:42 CDT)
- RE: constraint failure in Rattle algorithm for atom 54134 Tristan Croll (Mon Oct 26 2015 - 01:59:47 CDT)
  - Re: constraint failure in Rattle algorithm for atom 54134 Chitrak Gupta (Mon Oct 26 2015 - 09:10:59 CDT)
global does not work in configuration and callback function jc guo (Sat Oct 24 2015 - 01:46:21 CDT)
- AW: global does not work in configuration and callback function Norman Geist (Sat Oct 24 2015 - 08:30:48 CDT)
  - Re: global does not work in configuration and callback function jc guo (Sat Oct 24 2015 - 08:51:33 CDT)
NH4+ params Mikhail Suyetin (Fri Oct 23 2015 - 16:38:55 CDT)
- Re: NH4+ params Thomas Albers (Sat Oct 24 2015 - 09:26:17 CDT)
  - Re: Re: NH4+ params Mikhail Suyetin (Sat Oct 24 2015 - 11:56:15 CDT)
Dielectric constant of water from MSM and PME simulations Mattia Felice Palermo (Fri Oct 23 2015 - 08:57:37 CDT)
- Re: Dielectric constant of water from MSM and PME simulations Axel Kohlmeyer (Fri Oct 23 2015 - 09:47:38 CDT)
  - Re: Dielectric constant of water from MSM and PME simulations Zhe Wu (Fri Oct 23 2015 - 10:31:04 CDT)
    - Re: Dielectric constant of water from MSM and PME simulations Zhe Wu (Fri Oct 23 2015 - 10:46:41 CDT)
    - Re: Dielectric constant of water from MSM and PME simulations Otello Maria Roscioni (Mon Oct 26 2015 - 12:29:02 CDT)
GPU accelerated MD Nikhil Maroli (Fri Oct 23 2015 - 04:12:24 CDT)
- AW: GPU accelerated MD Norman Geist (Fri Oct 23 2015 - 05:00:05 CDT)
gromacs to charmm conversion Francesco Pietra (Fri Oct 23 2015 - 02:34:15 CDT)
- Re: vmd-l: gromacs to charmm conversion Ajasja LjubetiÄ (Fri Oct 23 2015 - 03:28:28 CDT)
aMD and GPU acceleration Thomas Albers (Thu Oct 22 2015 - 13:53:09 CDT)
Why the computational speed does not increase with the increase of GPUs? sunyeping (Wed Oct 21 2015 - 22:18:17 CDT)
- AW: Why the computational speed does not increase with the increase of GPUs? Norman Geist (Thu Oct 22 2015 - 02:27:54 CDT)
  - Re: AW: Why the computational speed does not increase with the increase of GPUs? sunyeping (Fri Oct 23 2015 - 02:57:48 CDT)
    - AW: Re: AW: Why the computational speed does not increase with the increase of GPUs? Norman Geist (Fri Oct 23 2015 - 03:49:49 CDT)
Error in Metadynamics Simulation Fidan Sumbul (Wed Oct 21 2015 - 16:31:30 CDT)
- Re: Error in Metadynamics Simulation Giacomo Fiorin (Thu Oct 22 2015 - 15:41:57 CDT)
  - Re: Error in Metadynamics Simulation Fidan Sumbul (Fri Oct 23 2015 - 06:08:40 CDT)
Topology for drugs to do MD after docking Nikhil Maroli (Wed Oct 21 2015 - 11:40:04 CDT)
- Re: Topology for drugs to do MD after docking Evandro Semighini (Wed Oct 21 2015 - 11:48:21 CDT)
- Re: vmd-l: Topology for drugs to do MD after docking Mayne, Christopher G (Wed Oct 21 2015 - 14:44:18 CDT)
ApoA1 simulation Kostas Malavazos (Wed Oct 21 2015 - 05:21:28 CDT)
(no subject) Mattia Felice Palermo (Wed Oct 21 2015 - 04:07:03 CDT)
Reverse Coarse Graining using VMD CG Builder Ardavan Mehdizadeh (Wed Oct 21 2015 - 03:15:35 CDT)
- Re: Reverse Coarse Graining using VMD CG Builder Peter Freddolino (Wed Oct 21 2015 - 07:29:13 CDT)
  - Re: Reverse Coarse Graining using VMD CG Builder Ardavan Mehdizadeh (Wed Oct 21 2015 - 10:41:55 CDT)
    - Re: Reverse Coarse Graining using VMD CG Builder Peter Freddolino (Wed Oct 21 2015 - 10:49:38 CDT)
  - Re: Reverse Coarse Graining using VMD CG Builder Peter Freddolino (Wed Oct 21 2015 - 11:25:44 CDT)
About the TMDInitialRMSD parameter in targeted molecular dynamics sunyeping (Tue Oct 20 2015 - 12:06:22 CDT)
Regarding FFTW routines usage in NAMD Puneet Singh (Tue Oct 20 2015 - 07:39:50 CDT)
- Re: Regarding FFTW routines usage in NAMD Axel Kohlmeyer (Tue Oct 20 2015 - 08:10:09 CDT)
AW: Regarding significance of days per ns (days/ns) parameter in NAMD benchmark Norman Geist (Tue Oct 20 2015 - 03:53:51 CDT)
Re: about re install sunyeping (Tue Oct 20 2015 - 02:09:33 CDT)
about re install jc guo (Tue Oct 20 2015 - 01:20:08 CDT)
Regarding significance of days per ns (days/ns) parameter in NAMD benchmark Puneet Singh (Tue Oct 20 2015 - 01:01:24 CDT)
- AW: Regarding significance of days per ns (days/ns) parameter in NAMD benchmark Norman Geist (Tue Oct 20 2015 - 01:29:19 CDT)
- Re: Regarding significance of days per ns (days/ns) parameter in NAMD benchmark Brian Radak (Tue Oct 20 2015 - 09:46:32 CDT)
How to calculate the temperature for a subset of my simulation Jhonatam Cordeiro Rodrigues (Mon Oct 19 2015 - 15:08:27 CDT)
- AW: How to calculate the temperature for a subset of my simulation Norman Geist (Tue Oct 20 2015 - 01:23:57 CDT)
  - Re: How to calculate the temperature for a subset of my simulation Jhonatam Cordeiro Rodrigues (Tue Oct 20 2015 - 12:20:46 CDT)
Several questions about targeted molecular dynamics sunyeping (Mon Oct 19 2015 - 04:54:09 CDT)
about command replicaRecv and replicaSend jc guo (Mon Oct 19 2015 - 02:09:43 CDT)
- AW: about command replicaRecv and replicaSend Norman Geist (Mon Oct 19 2015 - 02:43:43 CDT)
stepspercycle Gianluca Interlandi (Sun Oct 18 2015 - 20:20:26 CDT)
- AW: stepspercycle Norman Geist (Mon Oct 19 2015 - 01:25:18 CDT)
  - Re: AW: stepspercycle Gianluca Interlandi (Mon Oct 19 2015 - 12:31:23 CDT)
Bias-exchange metadynamics Fidan Sumbul (Sun Oct 18 2015 - 18:16:34 CDT)
Problem on merging multi-psf files into one wliu (Sun Oct 18 2015 - 07:52:11 CDT)
Performing MD simulations with protein and halide ions (iodide, bromide, chloride) Stojanoski, Vlatko (Sat Oct 17 2015 - 14:05:29 CDT)
- Re: Performing MD simulations with protein and halide ions (iodide, bromide, chloride) Branko (Sat Oct 17 2015 - 14:35:37 CDT)
  - Re: Performing MD simulations with protein and halide ions (iodide, bromide, chloride) Stojanoski, Vlatko (Sat Oct 17 2015 - 15:31:43 CDT)
    - Re: Performing MD simulations with protein and halide ions (iodide, bromide, chloride) Branko (Sat Oct 17 2015 - 15:42:11 CDT)
    - Re: Performing MD simulations with protein and halide ions (iodide, bromide, chloride) Stojanoski, Vlatko (Sat Oct 17 2015 - 15:49:19 CDT)
Rigid bonds and non-bonded energy Grzegorz Nawrocki (Fri Oct 16 2015 - 16:39:48 CDT)
- Re: Rigid bonds and non-bonded energy Brian Radak (Fri Oct 16 2015 - 17:42:34 CDT)
  - Re: Rigid bonds and non-bonded energy Brian Radak (Mon Oct 19 2015 - 14:40:51 CDT)
about replica exchange jc guo (Fri Oct 16 2015 - 10:43:23 CDT)
- Re: about replica exchange Jeff Comer (Fri Oct 16 2015 - 16:17:13 CDT)
NAMD - wrap atoms, not center of mass Stanislav Q=A0imko?= (Fri Oct 16 2015 - 10:20:28 CDT)
- Re: NAMD - wrap atoms, not center of mass Sourav Ray (Fri Oct 16 2015 - 10:27:09 CDT)
- Re: NAMD - wrap atoms, not center of mass Josh Vermaas (Fri Oct 16 2015 - 10:48:35 CDT)
about replica exchange example in lib of 2.10 NAMD jc guo (Fri Oct 16 2015 - 00:11:18 CDT)
- Re: about replica exchange example in lib of 2.10 NAMD Jeff Comer (Tue Oct 20 2015 - 20:10:00 CDT)
SMD or moving contraints Kevin C Chan (Thu Oct 15 2015 - 21:50:20 CDT)
Compile NAMD - Projections Kostas Malavazos (Wed Oct 14 2015 - 11:45:04 CDT)
- Re: Compile NAMD - Projections Stefan Richter (Thu Oct 15 2015 - 04:40:44 CDT)
keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Sridhar Kumar Kannam (Tue Oct 13 2015 - 23:39:14 CDT)
- Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. JÃ©rÃ´me HÃ©nin (Wed Oct 14 2015 - 05:05:54 CDT)
  - Re: keyword "outputaccumulatedwork" is not supported, or not recognized in this context. Marlon Sidore (Wed Oct 14 2015 - 05:12:16 CDT)
Compilation of NAMD from Source (Cray XC40) Richter, Stefan (Tue Oct 13 2015 - 09:26:06 CDT)
- Re: Compilation of NAMD from Source (Cray XC40) Jim Phillips (Tue Oct 13 2015 - 10:03:39 CDT)
  - AW: Compilation of NAMD from Source (Cray XC40) Richter, Stefan (Tue Oct 13 2015 - 13:10:44 CDT)
    - Re: Compilation of NAMD from Source (Cray XC40) Vlad Cojocaru (Tue Oct 13 2015 - 15:04:02 CDT)
    - Re: AW: Compilation of NAMD from Source (Cray XC40) Jim Phillips (Tue Oct 13 2015 - 17:00:08 CDT)
  - Re: Compilation of NAMD from Source (Cray XC40) Stefan Richter (Wed Oct 14 2015 - 04:38:17 CDT)
MD Simulation of accelerated MD using GPU jeevan gc (Mon Oct 12 2015 - 17:19:15 CDT)
- Re: MD Simulation of accelerated MD using GPU Brian Radak (Mon Oct 12 2015 - 20:01:24 CDT)
  - Re: MD Simulation of accelerated MD using GPU jeevan gc (Fri Oct 16 2015 - 08:25:29 CDT)
MD Simulation of accelerated MD using GPU jeevan gc (Mon Oct 12 2015 - 17:07:39 CDT)
- Re: MD Simulation of accelerated MD using GPU Kenneth Huang (Mon Oct 12 2015 - 20:09:26 CDT)
  - Re: MD Simulation of accelerated MD using GPU jeevan gc (Wed Oct 14 2015 - 16:21:36 CDT)
simulating TIP5P water Monika Madhavi (Fri Oct 09 2015 - 05:29:35 CDT)
- Re: simulating TIP5P water Peter Freddolino (Sat Oct 10 2015 - 21:33:50 CDT)
  - Re: simulating TIP5P water Monika Madhavi (Mon Oct 12 2015 - 03:44:50 CDT)
    - Re: simulating TIP5P water Monika Madhavi (Mon Oct 12 2015 - 05:10:35 CDT)
BONDS vs DOUBLE in topology file Gianluca Interlandi (Fri Oct 09 2015 - 00:42:05 CDT)
- Re: BONDS vs DOUBLE in topology file Josh Vermaas (Fri Oct 09 2015 - 09:46:07 CDT)
  - Re: BONDS vs DOUBLE in topology file Gianluca Interlandi (Fri Oct 09 2015 - 12:42:43 CDT)
about "small molecules" in OPLS-AAM FF Francesco Pietra (Wed Oct 07 2015 - 16:14:12 CDT)
Triple-hybrid topology? Tristan Croll (Tue Oct 06 2015 - 19:26:07 CDT)
Subscribe Vijay L. Roy (Tue Oct 06 2015 - 01:22:14 CDT)
Regarding biasTemperature used in Well-tempered metadynamics Vijay L. Roy (Tue Oct 06 2015 - 01:49:12 CDT)
- Re: Regarding biasTemperature used in Well-tempered metadynamics Giacomo Fiorin (Tue Oct 06 2015 - 09:01:52 CDT)
Coarse grained instability: atoms moving too fast Marlon Sidore (Mon Oct 05 2015 - 06:47:41 CDT)
Output to a file Mahdi Tavakol (Mon Oct 05 2015 - 01:31:55 CDT)
Segmentation Fault - Debug Kumar, Amit (Mon Oct 05 2015 - 09:13:14 CDT)
Regarding problem in psfgen of heparin siddharth kamal (Fri Oct 02 2015 - 14:20:15 CDT)
- RE: Regarding problem in psfgen of heparin Tristan Croll (Mon Oct 05 2015 - 23:00:32 CDT)
- Re: Regarding problem in psfgen of heparin Tristan Croll (Tue Oct 06 2015 - 18:44:21 CDT)
Ispopetide bond Milica UtjeÅ¡anoviÄ‡ (Fri Oct 02 2015 - 14:30:04 CDT)
Cyclic peptide Nanotube Nikhil Maroli (Fri Oct 02 2015 - 08:52:59 CDT)
script error Nikhil Maroli (Fri Oct 02 2015 - 08:44:13 CDT)
- Re: vmd-l: script error John Stone (Fri Oct 02 2015 - 10:10:56 CDT)
  - Re: Re: vmd-l: script error Nikhil Maroli (Sat Oct 03 2015 - 02:44:17 CDT)
PSF for cyclic peptide nanotube Nikhil Maroli (Fri Oct 02 2015 - 08:36:47 CDT)
simulating tip5p water Monika Madhavi (Thu Oct 01 2015 - 23:36:51 CDT)
Outward tilting which colvar to use Nicolas Martin (Thu Oct 01 2015 - 05:13:01 CDT)
- Re: Outward tilting which colvar to use JÃ©rÃ´me HÃ©nin (Thu Oct 01 2015 - 07:11:45 CDT)
Atomselect within radial pair distribution function g(r) Aditya Ranganathan (Wed Sep 30 2015 - 03:55:37 CDT)
- Re: Atomselect within radial pair distribution function g(r) Chitrak Gupta (Wed Sep 30 2015 - 08:09:16 CDT)
LJ Parameters on hydrogen for TIP4P water models Shayon Bhattacharya (Tue Sep 29 2015 - 10:20:36 CDT)
- Re: LJ Parameters on hydrogen for TIP4P water models Peter Freddolino (Tue Sep 29 2015 - 13:25:07 CDT)
  - Re: LJ Parameters on hydrogen for TIP4P water models Shayon Bhattacharya (Tue Sep 29 2015 - 14:04:44 CDT)
Hybrid coarse-grained/all-atom simulation Mahya Hemmat (Mon Sep 28 2015 - 14:25:24 CDT)
psf for cyclic peptide nanotube:psf ready for one ring but required for 8 ring Nikhil Maroli (Sat Sep 26 2015 - 06:50:31 CDT)
PSF for CYCLIC PEPTIDE : Nikhil Maroli (Sat Sep 26 2015 - 05:45:17 CDT)
- Re: PSF for CYCLIC PEPTIDE : bay__gulf618_at_sina.com (Sat Sep 26 2015 - 21:26:01 CDT)
Q=B4=D7=D4"=C2=C0=D0=A1=D3=A8"_<lv-xy11@mail?= s.tsinghua.edu.cn>µÄÓÊ¼þ ÂÀÐ¡Ó¨ (Fri Sep 25 2015 - 09:19:53 CDT)
Solvation free energy calculation with MM/GBSA Neelanjana Sengupta (Wed Sep 23 2015 - 06:51:28 CDT)
- Re: Solvation free energy calculation with MM/GBSA Abhishek TYAGI (Thu Sep 24 2015 - 07:13:20 CDT)
  - Re: Solvation free energy calculation with MM/GBSA Neelanjana Sengupta (Thu Sep 24 2015 - 07:37:04 CDT)
    - Re: Solvation free energy calculation with MM/GBSA Abhishek TYAGI (Thu Sep 24 2015 - 07:40:43 CDT)
- Re: Solvation free energy calculation with MM/GBSA Jeff Comer (Thu Sep 24 2015 - 08:27:26 CDT)
  - Re: Solvation free energy calculation with MM/GBSA Neelanjana Sengupta (Fri Sep 25 2015 - 07:36:50 CDT)
Re: Adaptive tempering implementation in NAMD differs Nicholas M. Glykos (Wed Sep 23 2015 - 05:45:40 CDT)
- Re: Adaptive tempering implementation in NAMD differs Sachin Natesh (Wed Sep 23 2015 - 10:28:05 CDT)
- Re: Adaptive tempering implementation in NAMD differs Sachin Natesh (Thu Sep 24 2015 - 20:28:36 CDT)
  - Re: Adaptive tempering implementation in NAMD differs Nicholas M Glykos (Fri Sep 25 2015 - 04:36:52 CDT)
Adaptive tempering implementation in NAMD differs from original paper? Sachin Natesh (Tue Sep 22 2015 - 19:45:22 CDT)
string method in NAMD 2.10 Jerry Karp (Mon Sep 21 2015 - 10:46:45 CDT)
string method in NAMD 2.10 Jerome Karp (Mon Sep 21 2015 - 10:49:42 CDT)
- Re: string method in NAMD 2.10 Thomas Evangelidis (Tue Sep 22 2015 - 05:29:16 CDT)
  - Re: string method in NAMD 2.10 Thomas Evangelidis (Tue Sep 22 2015 - 05:31:34 CDT)
Automatic PSF builder for cyclic peptide Nikhil Maroli (Sun Sep 20 2015 - 07:04:36 CDT)
- Re: Automatic PSF builder for cyclic peptide Aditya Ranganathan (Sun Sep 20 2015 - 08:20:24 CDT)
Which VMD AND NAMD should install Nikhil Maroli (Sat Sep 19 2015 - 01:57:30 CDT)
- Re: vmd-l: Which VMD AND NAMD should install John Stone (Tue Sep 22 2015 - 14:07:17 CDT)
NAMD Anisotropic pressure control Mahdi Tavakol (Fri Sep 18 2015 - 08:50:04 CDT)
- Re: NAMD Anisotropic pressure control JÃ©rÃ´me HÃ©nin (Fri Sep 18 2015 - 09:44:50 CDT)
  - Re: NAMD Anisotropic pressure control Mahdi Tavakol (Fri Sep 18 2015 - 11:51:29 CDT)
- Re: NAMD Anisotropic pressure control Fotis Baltoumas (Fri Sep 18 2015 - 09:50:14 CDT)
NAMD/VMD: generating psf for Abeta, ACE patch Mona Habibi (Tue Sep 15 2015 - 15:31:37 CDT)
- Re: NAMD/VMD: generating psf for Abeta, ACE patch Tristan Croll (Tue Sep 15 2015 - 17:53:20 CDT)
Can NAMD handle two different LJ cutoffs in a single simulation? Lewis Martin (Mon Sep 14 2015 - 23:17:36 CDT)
FEP utility for binding estimation HERBERT MAX VENTHUR PEÂ¥A (Mon Sep 14 2015 - 10:35:17 CDT)
simulating graphene sheets (with bonds across boundaries) with water upayan baul (Mon Sep 14 2015 - 06:59:00 CDT)
- Re: simulating graphene sheets (with bonds across boundaries) with water Abhishek TYAGI (Mon Sep 14 2015 - 19:28:04 CDT)
  - Re: simulating graphene sheets (with bonds across boundaries) with water upayan baul (Tue Sep 15 2015 - 06:57:20 CDT)
    - Re: simulating graphene sheets (with bonds across boundaries) with water Abhishek TYAGI (Tue Sep 15 2015 - 18:58:52 CDT)
- Re: simulating graphene sheets (with bonds across boundaries) with water Axel Kohlmeyer (Tue Sep 15 2015 - 19:22:27 CDT)
  - Re: simulating graphene sheets (with bonds across boundaries) with water upayan baul (Wed Sep 16 2015 - 05:40:38 CDT)
Parameterizing a novel peptide Bryan Roessler (Fri Sep 11 2015 - 17:14:05 CDT)
- Re: Parameterizing a novel peptide Tomek StÄ™pniewski (Fri Sep 11 2015 - 18:16:27 CDT)
  - Re: Parameterizing a novel peptide Mayne, Christopher G (Mon Sep 14 2015 - 08:48:57 CDT)
node file for NAMD Parag Khuraswar (Fri Sep 11 2015 - 08:02:54 CDT)
- Re: node file for NAMD Abhishek Tyagi (Fri Sep 11 2015 - 22:55:16 CDT)
  - Re: node file for NAMD Sourav Ray (Sat Sep 12 2015 - 01:11:30 CDT)
    - Re: node file for NAMD Sourav Ray (Sat Sep 12 2015 - 01:13:32 CDT)
Error in NAMD Controller Class Reference- Adaptive Tempering Sachin Natesh (Thu Sep 10 2015 - 19:13:41 CDT)
- Re: Error in NAMD Controller Class Reference- Adaptive Tempering Jeff Comer (Fri Sep 11 2015 - 08:10:02 CDT)
  - Re: Error in NAMD Controller Class Reference- Adaptive Tempering Jeff Comer (Fri Sep 11 2015 - 08:12:15 CDT)
Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech JC Gumbart (Wed Sep 09 2015 - 10:13:31 CDT)
- Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech JC Gumbart (Wed Sep 09 2015 - 18:15:34 CDT)
  - Re: vmd-l: Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech Sourav Ray (Wed Sep 09 2015 - 22:51:54 CDT)
    - Re: Re: vmd-l: Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech JC Gumbart (Fri Sep 11 2015 - 10:08:07 CDT)
    - Re: Re: vmd-l: Fwd: Inviting applications for a new PhD program in Quantitative Biosciences at Georgia Tech Sourav Ray (Fri Sep 11 2015 - 11:15:47 CDT)
charm36 for ATP and MG Radhika Anoop (Tue Sep 08 2015 - 00:55:48 CDT)
- Re: charm36 for ATP and MG Josh Vermaas (Tue Sep 08 2015 - 11:13:19 CDT)
  - Re: charm36 for ATP and MG Julian Gamboa (Tue Sep 08 2015 - 11:19:03 CDT)
    - Re: charm36 for ATP and MG Radhika Anoop (Wed Sep 09 2015 - 05:09:39 CDT)
Thermodynamic integration question Randall Hall (Sat Sep 05 2015 - 23:28:57 CDT)
- Re: Thermodynamic integration question JÃ©rÃ´me HÃ©nin (Mon Sep 07 2015 - 01:44:15 CDT)
"UNABLE TO FIND BOND PARAMETERS" but bond is defined in stream file Bryan Roessler (Fri Sep 04 2015 - 00:07:49 CDT)
- Re: "UNABLE TO FIND BOND PARAMETERS" but bond is defined in stream file Josh Vermaas (Fri Sep 04 2015 - 10:29:38 CDT)
patching SO3 group to GAG Lara rajam (Thu Sep 03 2015 - 19:13:21 CDT)
- Re: patching SO3 group to GAG Peter Freddolino (Thu Sep 03 2015 - 20:36:45 CDT)
  - Re: patching SO3 group to GAG Lara rajam (Thu Sep 03 2015 - 22:45:34 CDT)
node file for NAMD Parag Khuraswar (Tue Sep 01 2015 - 23:28:06 CDT)
parameters problem in sulfated molecules Lara rajam (Tue Sep 01 2015 - 12:12:42 CDT)
- Re: parameters problem in sulfated molecules Peter Freddolino (Tue Sep 01 2015 - 12:25:02 CDT)
- RE: parameters problem in sulfated molecules Bennion, Brian (Tue Sep 01 2015 - 12:27:17 CDT)
- Re: parameters problem in sulfated molecules siddharth kamal (Wed Sep 02 2015 - 08:33:11 CDT)
Reducing the amount of work being done on CPU Maxime Boissonneault (Tue Sep 01 2015 - 09:48:24 CDT)
- AW: Reducing the amount of work being done on CPU Norman Geist (Tue Sep 01 2015 - 12:47:56 CDT)
LJcorrection + switching? Brian Radak (Tue Sep 01 2015 - 09:31:34 CDT)
- Re: LJcorrection + switching? Peter Freddolino (Tue Sep 15 2015 - 20:11:32 CDT)
Sampling frequency Dr. Eddie (Mon Aug 31 2015 - 14:02:46 CDT)
- Re: Sampling frequency Jeff Comer (Tue Sep 01 2015 - 08:40:14 CDT)
Adaptive Tempering - Velocity Rescaling Sachin Natesh (Mon Aug 31 2015 - 09:45:16 CDT)
Atoms moving too fast; simulation has become unstable Monika Madhavi (Mon Aug 31 2015 - 05:42:48 CDT)
- Re: Atoms moving too fast; simulation has become unstable farzad kiani (Mon Aug 31 2015 - 06:17:38 CDT)
  - Re: Atoms moving too fast; simulation has become unstable Sourav Ray (Mon Aug 31 2015 - 06:29:30 CDT)
- Re: Atoms moving too fast; simulation has become unstable Peter Freddolino (Mon Aug 31 2015 - 08:30:48 CDT)
  - Re: Atoms moving too fast; simulation has become unstable Monika Madhavi (Thu Sep 17 2015 - 04:42:40 CDT)
heparin Lara rajam (Sat Aug 29 2015 - 18:48:08 CDT)
running namd gpu version Sanjana Anil Kumar Nair (Sat Aug 29 2015 - 05:21:41 CDT)
Problem running REMD simulation Nicholus Bhattacharjee (Tue Aug 25 2015 - 03:01:36 CDT)
- AW: Problem running REMD simulation Norman Geist (Tue Aug 25 2015 - 03:50:15 CDT)
- Re: Problem running REMD simulation Douglas Houston (Tue Aug 25 2015 - 04:16:55 CDT)
  - Re: Problem running REMD simulation Nicholus Bhattacharjee (Tue Aug 25 2015 - 04:59:07 CDT)
    - Re: Problem running REMD simulation Peter Freddolino (Tue Aug 25 2015 - 23:25:00 CDT)
  - Re: Problem running REMD simulation Peter Freddolino (Wed Aug 26 2015 - 08:28:57 CDT)
    - Re: Problem running REMD simulation Nicholus Bhattacharjee (Thu Aug 27 2015 - 03:00:31 CDT)
    - AW: Problem running REMD simulation Norman Geist (Thu Aug 27 2015 - 03:42:10 CDT)
Format of colvars.state Hossein Mohammadiarani (Mon Aug 24 2015 - 12:53:14 CDT)
- Re: Format of colvars.state JÃ©rÃ´me HÃ©nin (Mon Aug 24 2015 - 13:04:50 CDT)
  - Re: Format of colvars.state Hossein Mohammadiarani (Wed Aug 26 2015 - 18:05:19 CDT)
    - Re: Format of colvars.state JÃ©rÃ´me HÃ©nin (Thu Aug 27 2015 - 04:27:00 CDT)
Problem with iron ion (FE2+) Daniela Rivas (Mon Aug 24 2015 - 12:51:59 CDT)
- Re: Problem with iron ion (FE2+) Branko (Mon Aug 24 2015 - 13:09:01 CDT)
  - Re: Problem with iron ion (FE2+) Daniela Rivas (Mon Aug 24 2015 - 13:16:15 CDT)
feature request: external initiated clean exit Daniel Möller (Fri Aug 21 2015 - 07:37:02 CDT)
- RE: feature request: external initiated clean exit Parag Khuraswar (Fri Aug 21 2015 - 07:58:53 CDT)
  - Re: feature request: external initiated clean exit Peter Freddolino (Fri Aug 21 2015 - 16:47:55 CDT)
- Re: feature request: external initiated clean exit Peter Freddolino (Fri Aug 21 2015 - 16:44:27 CDT)
  - Re: feature request: external initiated clean exit Axel Kohlmeyer (Fri Aug 21 2015 - 17:03:32 CDT)
Problem running REMD simulation Nicholus Bhattacharjee (Thu Aug 20 2015 - 03:47:33 CDT)
Charm++ warning> fences and atomic operations not available in native assembly Ern Seang Ong (Thu Aug 20 2015 - 02:56:40 CDT)
Lambda-exchange multiple-copy alchemical free energy calculations å²¡éƒ¨ç¯¤ä¿Š (Tue Aug 18 2015 - 09:54:40 CDT)
Regarding NAMD installation Pragya Priyadarshini (Mon Aug 17 2015 - 02:45:13 CDT)
- Re: Regarding NAMD installation Sourav Ray (Mon Aug 17 2015 - 02:53:00 CDT)
- AW: Regarding NAMD installation Norman Geist (Mon Aug 17 2015 - 04:32:19 CDT)
  - Re: AW: Regarding NAMD installation Pragya Priyadarshini (Mon Aug 17 2015 - 04:38:29 CDT)
    - AW: AW: Regarding NAMD installation Norman Geist (Mon Aug 17 2015 - 05:22:11 CDT)
Looking for benchmarks on k80's rswett_at_chem.wayne.edu (Thu Aug 13 2015 - 10:40:45 CDT)
PME Seg Fault Richard Overstreet (Mon Aug 10 2015 - 09:11:27 CDT)
- Re: PME Seg Fault Vibhor Agrawal (Mon Aug 10 2015 - 11:31:56 CDT)
Verification of NAMD Results Kanzliersch, Lukas (Wed Aug 05 2015 - 15:32:38 CDT)
OPLS/AA force field oguz gurbulak (Wed Aug 05 2015 - 09:00:01 CDT)
eBiothon platform eBiothon Admin Team (Mon Aug 03 2015 - 10:07:36 CDT)
Re: namd-l digest V1 #1726 nader zabarjad (Sun Aug 02 2015 - 10:41:55 CDT)
how to create two namd jobs in a single script with 2 x dual cuda gpus? nam kim (Sat Aug 01 2015 - 16:36:15 CDT)
Re: how to create two namd jobs in a single script with 2 x dual cuda gpus? nam kim (Sat Aug 01 2015 - 16:33:04 CDT)
sausage plot for a namd trajectory in vmd luca belmonte (Fri Jul 31 2015 - 05:01:02 CDT)
- Re: sausage plot for a namd trajectory in vmd Aaron Larsen (Fri Jul 31 2015 - 05:44:17 CDT)
  - Re: sausage plot for a namd trajectory in vmd Thomas C. Bishop (Tue Aug 11 2015 - 10:30:23 CDT)
Metadynamics: writeHillsTrajectory Chola Regmi (Thu Jul 30 2015 - 16:37:53 CDT)
- Re: Metadynamics: writeHillsTrajectory Chola Regmi (Thu Jul 30 2015 - 16:48:15 CDT)
run NAMD 2.10 on Xeon Phi machine Xiaoge Wang (Tue Jul 28 2015 - 12:50:23 CDT)
The 2 NAMD tests "Alanin" and "tclforces" fail to run with "Atoms moving too fast" error Sriram Adhyapak (Mon Jul 27 2015 - 20:36:14 CDT)
"missing operator at _@_ in expression" for if statement Simon Kit Sang Chu (Mon Jul 27 2015 - 19:39:51 CDT)
- RE: "missing operator at _@_ in expression" for if statement Norman Geist (Tue Jul 28 2015 - 01:33:01 CDT)
Interrupted Molecular Dynamics Simulation Daniela Rivas (Mon Jul 27 2015 - 10:32:29 CDT)
- Re: Interrupted Molecular Dynamics Simulation Chitrak Gupta (Mon Jul 27 2015 - 12:29:25 CDT)
  - Re: Interrupted Molecular Dynamics Simulation Daniela Rivas (Mon Jul 27 2015 - 19:21:00 CDT)
NAMD hybrid configuration: Atoms moving too fast error Puneet Singh (Mon Jul 27 2015 - 06:41:38 CDT)
Instability in harmonic restraints when equilibrating large systems Tristan Croll (Fri Jul 24 2015 - 16:52:05 CDT)
Patch-size Error (not like the other ones) Merrill, Dante (Fri Jul 24 2015 - 13:14:28 CDT)
- Re: Patch-size Error (not like the other ones) Jeffrey Potoff (Fri Jul 24 2015 - 13:38:52 CDT)
- RE: Patch-size Error (not like the other ones) Norman Geist (Mon Jul 27 2015 - 02:32:33 CDT)
segmentation fault when running with mpirun Puneet Singh (Fri Jul 24 2015 - 08:05:23 CDT)
Tilt angle clockwise rotation Nicolas Martin (Wed Jul 22 2015 - 08:34:47 CDT)
- Re: Tilt angle clockwise rotation JÃ©rÃ´me HÃ©nin (Wed Jul 22 2015 - 11:04:55 CDT)
FEP method- Free energy of solvation of ligand Mohan maruthi sena (Wed Jul 22 2015 - 02:25:40 CDT)
- backbone constraint Urszula Uciechowska (Wed Jul 22 2015 - 02:59:37 CDT)
  - Re: backbone constraint Josh Vermaas (Wed Jul 22 2015 - 08:59:48 CDT)
    - FATAL ERROR: Incorrect atom count in binary file min.coor Urszula Uciechowska (Fri Jul 24 2015 - 03:27:31 CDT)
- Re: FEP method- Free energy of solvation of ligand Felipe Merino (Wed Jul 22 2015 - 03:07:32 CDT)
- RE: FEP method- Free energy of solvation of ligand hannes.loeffler_at_stfc.ac.uk (Wed Jul 22 2015 - 03:10:42 CDT)
wrapping in NVT Abhishek TYAGI (Tue Jul 21 2015 - 22:59:52 CDT)
- Re: wrapping in NVT Richard Overstreet (Wed Jul 22 2015 - 01:05:30 CDT)
  - Re: wrapping in NVT Abhishek TYAGI (Wed Jul 22 2015 - 00:27:02 CDT)
Error in TI derivatives for staggered lambda scaling? Brian Radak (Tue Jul 21 2015 - 13:41:28 CDT)
restart error Lara rajam (Mon Jul 20 2015 - 10:15:23 CDT)
Debugging and Force Checking? Brian Radak (Mon Jul 20 2015 - 09:32:44 CDT)
- Re: Debugging and Force Checking? JÃ©rÃ´me HÃ©nin (Mon Jul 20 2015 - 12:42:20 CDT)
Compilation with OpenMPI Kevin C Chan (Mon Jul 20 2015 - 05:02:10 CDT)
VDW energy diverged & VMD functions applied on cluster Simon Kit Sang Chu (Sat Jul 18 2015 - 16:37:54 CDT)
what exactly is the form of the cosine angle potential? Charlesworth, Henry (Fri Jul 17 2015 - 08:08:50 CDT)
- Re: what exactly is the form of the cosine angle potential? Fotis Baltoumas (Fri Jul 17 2015 - 08:47:55 CDT)
Minimization without MD Simon Kit Sang Chu (Thu Jul 16 2015 - 15:37:39 CDT)
- Re: Minimization without MD Ajasja LjubetiÄ (Thu Jul 16 2015 - 17:18:20 CDT)
Minimization without MD Simon Kit Sang Chu (Thu Jul 16 2015 - 16:21:40 CDT)
Controlling water diffusion Evandro Semighini (Thu Jul 16 2015 - 14:21:50 CDT)
- Re: Controlling water diffusion Peter Freddolino (Thu Jul 16 2015 - 21:54:49 CDT)
  - Re: Controlling water diffusion Evandro Semighini (Fri Jul 17 2015 - 07:44:36 CDT)
namd ibverbs Maxime Boissonneault (Thu Jul 16 2015 - 12:59:50 CDT)
- Re: namd ibverbs Gianluca Interlandi (Thu Jul 16 2015 - 15:31:34 CDT)
  - Re: namd ibverbs Maxime Boissonneault (Thu Jul 16 2015 - 15:50:36 CDT)
Fwd: Regarding problem in generating psf file of heparin and heparan sulfate siddharth kamal (Thu Jul 16 2015 - 07:44:46 CDT)
- protein-DNA complex Urszula Uciechowska (Thu Jul 16 2015 - 09:40:25 CDT)
  - Re: protein-DNA complex Vlad Cojocaru (Thu Jul 16 2015 - 10:59:19 CDT)
Compilation with OpenMPI Kevin C Chan (Tue Jul 14 2015 - 00:11:38 CDT)
UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT Anjela Manandhar (Mon Jul 13 2015 - 15:58:55 CDT)
Compilation with OpenMPI Kevin C Chan (Sun Jul 12 2015 - 01:13:30 CDT)
Running constant pH molecular dynamics (CpHMD) Leonardo Herrera (Thu Jul 09 2015 - 19:00:02 CDT)
- Re: Running constant pH molecular dynamics (CpHMD) Jason Swails (Thu Jul 09 2015 - 20:05:36 CDT)
call "NAMD" from another program Ma'Mon Hatmal (Thu Jul 09 2015 - 17:53:24 CDT)
- Re: call "NAMD" from another program Aron Broom (Thu Jul 09 2015 - 17:59:08 CDT)
- NAMD workflows <- : Re: call "NAMD" from another program Thomas C Bishop (Fri Jul 10 2015 - 02:38:00 CDT)
  - Re: NAMD workflows <- : Re: call "NAMD" from another program Ajasja LjubetiÄ (Fri Jul 10 2015 - 02:50:31 CDT)
- Re: call "NAMD" from another program bay__gulf618_at_sina.com (Sat Jul 11 2015 - 22:21:09 CDT)
model.conf Mai Aamer (Thu Jul 09 2015 - 17:09:01 CDT)
NAMD 2.10 Building from Source Kumar, Amit (Thu Jul 09 2015 - 15:28:07 CDT)
- Re: NAMD 2.10 Building from Source Giacomo Fiorin (Thu Jul 09 2015 - 15:45:32 CDT)
  - RE: NAMD 2.10 Building from Source Kumar, Amit (Thu Jul 09 2015 - 16:02:07 CDT)
    - Re: NAMD 2.10 Building from Source Giacomo Fiorin (Thu Jul 09 2015 - 16:05:02 CDT)
polymerization simulations L. Signorile (Thu Jul 09 2015 - 13:06:51 CDT)
- Re: polymerization simulations Giacomo Fiorin (Thu Jul 09 2015 - 15:51:38 CDT)
does fixedAtoms modify velocities? Brian Radak (Tue Jul 07 2015 - 12:25:32 CDT)
- Re: does fixedAtoms modify velocities? Brian Radak (Tue Jul 07 2015 - 12:48:23 CDT)
-xHost Gianluca Interlandi (Mon Jul 06 2015 - 13:08:37 CDT)
Error: Constraint failure in RATTLE algorithm for atom 5380! in NAMD Mahya Hemmat (Mon Jul 06 2015 - 11:06:39 CDT)
Generating solvent models. VINAYAK BHAT (Sun Jul 05 2015 - 04:06:27 CDT)
running multicore version on a 2-CPU node Gianluca Interlandi (Sat Jul 04 2015 - 15:33:25 CDT)
multicore vs ibverbs Gianluca Interlandi (Sat Jul 04 2015 - 12:52:40 CDT)
extra bonds Lara rajam (Thu Jul 02 2015 - 09:20:59 CDT)
- Re: extra bonds Josh Vermaas (Thu Jul 02 2015 - 09:48:22 CDT)
  - Re: extra bonds Lara rajam (Thu Jul 02 2015 - 12:35:14 CDT)
    - Re: extra bonds Josh Vermaas (Fri Jul 03 2015 - 09:08:25 CDT)
Re: replica exchange and GPU acceleration Mitchell Gleed (Wed Jul 01 2015 - 11:01:50 CDT)
- RE: replica exchange and GPU acceleration Norman Geist (Fri Jul 03 2015 - 03:16:17 CDT)
- Re: replica exchange and GPU acceleration Mitchell Gleed (Sat Jul 04 2015 - 10:49:22 CDT)
  - RE: replica exchange and GPU acceleration Norman Geist (Mon Jul 06 2015 - 01:38:11 CDT)
- Re: replica exchange and GPU acceleration Mitchell Gleed (Sun Jul 12 2015 - 22:36:54 CDT)
  - RE: replica exchange and GPU acceleration Norman Geist (Mon Jul 13 2015 - 00:51:11 CDT)
- Re: replica exchange and GPU acceleration Mitchell Gleed (Mon Jul 13 2015 - 01:32:14 CDT)
statistical error of mean force in (NAMD) ABF calculations Branko (Wed Jul 01 2015 - 05:09:48 CDT)
- Re: statistical error of mean force in (NAMD) ABF calculations Jeff Comer (Thu Jul 02 2015 - 09:09:38 CDT)
replica exchange and GPU acceleration Mitchell Gleed (Tue Jun 30 2015 - 18:09:27 CDT)
- RE: replica exchange and GPU acceleration Norman Geist (Wed Jul 01 2015 - 02:13:56 CDT)
Attempting modification to accumulate "Langevin heat" Brian Radak (Tue Jun 30 2015 - 10:43:40 CDT)
Re: I can not run fixed protein in membrane with NAMD R.L. Ma (Sat Jun 27 2015 - 21:27:18 CDT)
- Re: Re: I can not run fixed protein in membrane with NAMD Chitrak Gupta (Mon Jun 29 2015 - 14:41:11 CDT)
applying a force to some atoms jing liang (Sat Jun 27 2015 - 06:22:02 CDT)
- Re: applying a force to some atoms JÃ©rÃ´me HÃ©nin (Sun Jun 28 2015 - 15:54:42 CDT)
Pressure coupling options Kevin C Chan (Fri Jun 26 2015 - 23:32:05 CDT)
- Re: Pressure coupling options Josh Vermaas (Sat Jun 27 2015 - 19:36:17 CDT)
  - Re: Pressure coupling options Chitrak Gupta (Sun Jun 28 2015 - 15:54:05 CDT)
not able to view trajectory in VMD Lara rajam (Fri Jun 26 2015 - 12:55:01 CDT)
- Re: not able to view trajectory in VMD Axel Kohlmeyer (Fri Jun 26 2015 - 13:04:20 CDT)
Minimisation goes to several values Kevin C Chan (Thu Jun 25 2015 - 11:32:10 CDT)
NAMD 2.10 on IBM POWER(8) machines Baker D.J. (Thu Jun 25 2015 - 07:00:49 CDT)
free energy calculation along image index in us ÂÀÐ¡Ó¨ (Wed Jun 24 2015 - 02:27:35 CDT)
- run on sungle node Alexander Tzanov (Wed Jun 24 2015 - 09:56:18 CDT)
  - Re: run on sungle node Alexander Tzanov (Wed Jun 24 2015 - 11:03:24 CDT)
bond lengths and angles constraints oguz gurbulak (Tue Jun 23 2015 - 10:04:53 CDT)
Getting Infinity in Calculation of Free Energy using SMD Ebru Ã‡etin (Tue Jun 23 2015 - 00:23:19 CDT)
Re: Create psf file Mayne, Christopher G (Mon Jun 22 2015 - 10:01:23 CDT)
Create psf file Fransiska Kurniawan (Sat Jun 20 2015 - 17:56:52 CDT)
- RE: Create psf file Raed Ahmed Abdelsalam Shalaby (Mon Jun 22 2015 - 05:54:32 CDT)
- Re: Create psf file Asma el-magboub (Mon Jun 22 2015 - 18:43:13 CDT)
OPLS force field in NAMD oguz gurbulak (Sat Jun 20 2015 - 11:43:02 CDT)
- Re: OPLS force field in NAMD farzad kiani (Sat Jun 20 2015 - 15:28:39 CDT)
  - Re: OPLS force field in NAMD AnkiReddy katha (Sat Jun 20 2015 - 16:17:31 CDT)
- Re: OPLS force field in NAMD Peter Freddolino (Sat Jun 20 2015 - 22:20:00 CDT)
Weird Bond In Non-Polar Tail Danielle Grodi (Thu Jun 18 2015 - 10:15:53 CDT)
- Re: Weird Bond In Non-Polar Tail Axel Kohlmeyer (Thu Jun 18 2015 - 10:45:06 CDT)
Remembering resid Kevin C Chan (Thu Jun 18 2015 - 08:42:34 CDT)
- Re: Remembering resid Branko (Thu Jun 18 2015 - 08:54:40 CDT)
- Re: Remembering resid Chitrak Gupta (Thu Jun 18 2015 - 08:52:08 CDT)
  - Re: Remembering resid Kevin C Chan (Thu Jun 18 2015 - 11:48:50 CDT)
Second Announcement: â€˜Hands Onâ€™ Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015) Lela Vukovic (Tue Jun 16 2015 - 12:04:27 CDT)
Fwd: Re: Combining parameter files from CHARMM Branko (Mon Jun 15 2015 - 05:12:57 CDT)
Announcement: Workshop on Simulation Based Drug Discovery (San Diego, CA, Sept 21-25, 2015) Lela Vukovic (Fri Jun 12 2015 - 21:06:22 CDT)
Multiple-replicas metadynamics / Well-tempered metadynamics Yerko Escalona (Fri Jun 12 2015 - 14:15:39 CDT)
- Re: Multiple-replicas metadynamics / Well-tempered metadynamics Giacomo Fiorin (Fri Jun 12 2015 - 14:21:15 CDT)
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CTL2 OC301 (ATOMS 25 45) Danielle Grodi (Fri Jun 12 2015 - 13:39:30 CDT)
- Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR CTL2 OC301 (ATOMS 25 45) Sourav Ray (Fri Jun 12 2015 - 13:49:00 CDT)
non-bonded energy of individual atoms Bärwinkel, Tom (Fri Jun 12 2015 - 09:17:46 CDT)
Using a different potential with NAMD Wade, Alex (Fri Jun 12 2015 - 09:08:48 CDT)
- Re: Using a different potential with NAMD Peter Freddolino (Fri Jun 12 2015 - 09:25:32 CDT)
- Re: Using a different potential with NAMD Axel Kohlmeyer (Fri Jun 12 2015 - 09:39:47 CDT)
Recomposing the system splitted by periodicity Francesco Pietra (Thu Jun 11 2015 - 04:34:57 CDT)
- Re: Recomposing the system splitted by periodicity Tristan Croll (Thu Jun 11 2015 - 23:22:50 CDT)
Constant velocity SMD maral hassani (Tue Jun 09 2015 - 07:14:16 CDT)
FFTK - error Mayne, Christopher G (Mon Jun 08 2015 - 11:56:34 CDT)
Postdoc in Theoretical and Computational Biophysics Aksimentiev, Oleksii (Mon Jun 08 2015 - 11:51:11 CDT)
electrostatics cutoff parameters Z (Mon Jun 08 2015 - 09:06:00 CDT)
FFTK - error Mohan maruthi sena (Sat Jun 06 2015 - 18:35:44 CDT)
Combining parameter files from CHARMM Kevin C Chan (Fri Jun 05 2015 - 04:51:13 CDT)
- Re: Combining parameter files from CHARMM Branko (Fri Jun 05 2015 - 05:17:56 CDT)
  - Re: Combining parameter files from CHARMM Kevin C Chan (Mon Jun 15 2015 - 03:08:06 CDT)
    - Why the Lennardâˆ’Jones parameters E for anions are usually larger than cations? bay__gulf618_at_sina.com (Mon Jun 15 2015 - 04:02:44 CDT)
    - Re: Why the Lennardâˆ’Jones parameters E for anions are usually larger than cations? Axel Kohlmeyer (Mon Jun 15 2015 - 05:36:16 CDT)
  - Re: Combining parameter files from CHARMM Kevin C Chan (Mon Jun 15 2015 - 07:29:36 CDT)
    - Re: Combining parameter files from CHARMM Branko (Mon Jun 15 2015 - 07:39:49 CDT)
    - Re: Combining parameter files from CHARMM Josh Vermaas (Mon Jun 15 2015 - 11:10:43 CDT)
error in writing colvars state file Bennion, Brian (Thu Jun 04 2015 - 16:24:44 CDT)
- RE: error in writing colvars state file Bennion, Brian (Thu Jun 04 2015 - 16:30:07 CDT)
  - Re: RE: error in writing colvars state file JÃ©rÃ´me HÃ©nin (Fri Jun 05 2015 - 05:33:07 CDT)
Colvars Boundary potentials do not look harmonic Panel Nicolas (M.) (Wed Jun 03 2015 - 10:00:53 CDT)
- Re: Colvars Boundary potentials do not look harmonic JÃ©rÃ´me HÃ©nin (Wed Jun 03 2015 - 10:15:04 CDT)
  - Re: Colvars Boundary potentials do not look harmonic Jeff Comer (Wed Jun 03 2015 - 11:54:28 CDT)
    - Re: Colvars Boundary potentials do not look harmonic Panel Nicolas (M.) (Thu Jun 04 2015 - 08:08:49 CDT)
Using the multi-copy version of NAMD on a linux workstation Avisek Das (Fri May 29 2015 - 14:43:18 CDT)
- RE: Using the multi-copy version of NAMD on a linux workstation Norman Geist (Mon Jun 01 2015 - 02:43:36 CDT)
  - RE: Using the multi-copy version of NAMD on a linux workstation Avisek Das (Mon Jun 01 2015 - 12:22:46 CDT)
NAMD-Replica exchange ZOU Changling (Wed May 27 2015 - 04:31:28 CDT)
Can 'nonbonded interaction parameters' be ignored in the parameter file? ¶¡êÏ (Tue May 26 2015 - 20:43:52 CDT)
the method to move freely in one direction like a rigid body Xiaokang Liu (Mon May 25 2015 - 05:46:40 CDT)
running with replica exchange on stampede Peter Freddolino (Sun May 24 2015 - 21:40:09 CDT)
where can I find the parameter file for chlorophenols? ¶¡êÏ (Sun May 24 2015 - 08:30:15 CDT)
- Re: where can I find the parameter file for chlorophenols? Jeff Comer (Mon May 25 2015 - 14:35:46 CDT)
Force-field for DOPI lipid Kevin C Chan (Sat May 23 2015 - 13:58:30 CDT)
- Re: Force-field for DOPI lipid Josh Vermaas (Sun May 24 2015 - 08:27:46 CDT)
atom types in PSF/PRM/RTF Hannes Loeffler (Fri May 22 2015 - 04:42:45 CDT)
- Re: atom types in PSF/PRM/RTF Aaron Larsen (Fri May 22 2015 - 07:34:37 CDT)
  - Re: atom types in PSF/PRM/RTF Josh Vermaas (Fri May 22 2015 - 09:55:44 CDT)
Error during Opt. Charges while using FF Took Kit Aaron Larsen (Wed May 20 2015 - 16:38:19 CDT)
Restarting trajectories Michael Feig (Wed May 20 2015 - 02:47:08 CDT)
- RE: Restarting trajectories Bennion, Brian (Wed May 20 2015 - 10:42:46 CDT)
- Re: Restarting trajectories Axel Kohlmeyer (Wed May 20 2015 - 10:49:11 CDT)
  - RE: Restarting trajectories Michael Feig (Wed May 20 2015 - 10:59:07 CDT)
Best Practices for Nucleobase Parameterization Mayne, Christopher G (Wed May 20 2015 - 08:12:55 CDT)
Restarting trajectories Michael Feig (Wed May 20 2015 - 03:01:37 CDT)
Announcement: â€˜Hands Onâ€™ Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015) Lela Vukovic (Wed May 20 2015 - 00:06:46 CDT)
- Re: Announcement: 'Hands On' Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015) Sourav Ray (Wed May 20 2015 - 00:33:00 CDT)
  - Re: Announcement: 'Hands On' Workshop on Computational Biophysics (Berkeley, CA, Aug 3-7, 2015) Emad Tajkhorshid (Wed May 20 2015 - 00:43:55 CDT)
Best Practices for Nucleobase Parameterization Aaron Larsen (Mon May 18 2015 - 11:30:22 CDT)
Re: optimising namd ibverb runs Aaron Larsen (Mon May 18 2015 - 08:48:18 CDT)
optimising namd ibverb runs Thanassis Silis (Mon May 18 2015 - 06:48:03 CDT)
- RE: optimising namd ibverb runs Norman Geist (Mon May 18 2015 - 08:16:11 CDT)
- Re: optimising namd ibverb runs Jim Phillips (Wed May 20 2015 - 12:28:37 CDT)
Different trajectories with and without restarting Grzegorz Nawrocki (Fri May 15 2015 - 18:09:57 CDT)
- Re: Different trajectories with and without restarting btreece_at_andrew.cmu.edu (Fri May 15 2015 - 18:26:09 CDT)
- Re: Different trajectories with and without restarting Axel Kohlmeyer (Fri May 15 2015 - 18:26:53 CDT)
  - Re: Different trajectories with and without restarting Grzegorz Nawrocki (Fri May 15 2015 - 21:08:40 CDT)
    - Re: Different trajectories with and without restarting Axel Kohlmeyer (Sat May 16 2015 - 00:06:27 CDT)
    - Re: Different trajectories with and without restarting Grzegorz Nawrocki (Mon May 18 2015 - 15:04:17 CDT)
+p option on Windows 7 Kukol, Andreas (Fri May 15 2015 - 05:07:55 CDT)
- RE: +p option on Windows 7 Norman Geist (Mon May 18 2015 - 02:39:30 CDT)
- Re: +p option on Windows 7 Jim Phillips (Wed May 20 2015 - 11:58:13 CDT)
Re: Error applying PME to simulation set up Sourav Ray (Wed May 13 2015 - 06:02:51 CDT)
- Re: Error applying PME to simulation set up Axel Kohlmeyer (Wed May 13 2015 - 08:00:00 CDT)
Error applying PME to simulation set up Sourav Ray (Wed May 13 2015 - 04:24:41 CDT)
- RE: Error applying PME to simulation set up Norman Geist (Wed May 13 2015 - 05:08:45 CDT)
startup phase 1 for benchmark Branko (Tue May 12 2015 - 09:29:28 CDT)
NAMD Repeated failures launching tasks Kumar, Amit (Mon May 11 2015 - 13:47:40 CDT)
Calculating the spin angle collective variable value Marlon SIDORE (Mon May 11 2015 - 03:51:38 CDT)
- Re: Calculating the spin angle collective variable value Giacomo Fiorin (Mon May 11 2015 - 08:40:34 CDT)
  - Re: Calculating the spin angle collective variable value Marlon SIDORE (Mon May 11 2015 - 08:48:51 CDT)
    - Re: Calculating the spin angle collective variable value Giacomo Fiorin (Mon May 11 2015 - 08:57:41 CDT)
    - Re: Calculating the spin angle collective variable value Marlon SIDORE (Mon May 11 2015 - 09:06:46 CDT)
Processing 64-window FEP Matthew Ralph Adendorff (Sun May 10 2015 - 08:44:08 CDT)
School on Molecular Dynamics and Enhanced Sampling Methods @ Temple University July 6-10, 2015 Axel Kohlmeyer (Fri May 08 2015 - 11:28:54 CDT)
OPLS force-field in NAMD AnkiReddy katha (Thu May 07 2015 - 02:12:03 CDT)
output files are not stored when running namd-2.10 ibverbs Thanassis Silis (Thu May 07 2015 - 10:29:26 CDT)
- RE: output files are not stored when running namd-2.10 ibverbs Thanassis Silis (Fri May 08 2015 - 05:07:50 CDT)
atoms sequence in improper, OPLS, TOPOTOOLS, CHARMM AnkiReddy katha (Thu May 07 2015 - 06:17:27 CDT)
Re: OPLS in NAMD AnkiReddy katha (Thu May 07 2015 - 04:40:47 CDT)
OPLS in NAMD AnkiReddy katha (Thu May 07 2015 - 04:17:23 CDT)
PSFgen with RNA-like nucleotide monophosphates Aaron Larsen (Wed May 06 2015 - 11:01:26 CDT)
Announcement: â€˜Hands Onâ€™ Workshop on Computational Biophysics (Odense, Denmark, Oct 12-16, 2015) Lela Vukovic (Wed May 06 2015 - 01:39:55 CDT)
Simulation Box Rescaling Phillips, Carolyn L. (Tue May 05 2015 - 18:02:28 CDT)
atom ID in VMD and NAMD Maxim Igaev (Mon May 04 2015 - 03:16:09 CDT)
- Re: atom ID in VMD and NAMD JÃ©rÃ´me HÃ©nin (Mon May 04 2015 - 04:52:06 CDT)
  - Re: atom ID in VMD and NAMD Maxim Igaev (Mon May 04 2015 - 06:47:09 CDT)
RE: namd-l digest V1 #1668 Ern Seang Ong (Sun May 03 2015 - 23:14:28 CDT)
- RE: namd-l digest V1 #1668 Bennion, Brian (Mon May 04 2015 - 10:42:12 CDT)
mail reg DCD error Vidhya Sankar (Sun May 03 2015 - 09:44:50 CDT)
proper order for par files in namd Mayne, Christopher G (Fri May 01 2015 - 09:21:11 CDT)
Problems in running AutoIMD Ern Seang Ong (Thu Apr 30 2015 - 23:33:47 CDT)
- RE: Problems in running AutoIMD Bennion, Brian (Fri May 01 2015 - 11:00:35 CDT)
Simulated Annealing with many frequent restarts Phillips, Carolyn L. (Thu Apr 30 2015 - 18:51:19 CDT)
- Re: Simulated Annealing with many frequent restarts Francesco Pietra (Fri May 01 2015 - 01:21:28 CDT)
- Re: Simulated Annealing with many frequent restarts Maxim Belkin (Fri May 01 2015 - 09:46:21 CDT)
  - Re: Simulated Annealing with many frequent restarts Phillips, Carolyn L. (Fri May 01 2015 - 10:16:43 CDT)
performance question Thomas C. Bishop (Mon Apr 27 2015 - 15:54:10 CDT)
- RE: performance question Norman Geist (Tue Apr 28 2015 - 02:51:06 CDT)
  - Re: performance question Thomas C. Bishop (Tue Apr 28 2015 - 14:32:16 CDT)
question about restart conf file oguz gurbulak (Sun Apr 26 2015 - 07:10:44 CDT)
RE: proper order for par files in namd (solved) Bennion, Brian (Fri Apr 24 2015 - 18:21:22 CDT)
proper order for par files in namd Bennion, Brian (Fri Apr 24 2015 - 17:05:16 CDT)
Patches for namd 2.10 Ã…ke Sandgren (Fri Apr 24 2015 - 01:09:35 CDT)
- Re: Patches for namd 2.10 JÃ©rÃ´me HÃ©nin (Fri Apr 24 2015 - 04:38:39 CDT)
  - Re: Patches for namd 2.10 Ã…ke Sandgren (Fri Apr 24 2015 - 06:06:53 CDT)
Which Binary to use? Arijit Ghosh (Fri Apr 24 2015 - 00:10:49 CDT)
- Re: Which Binary to use? Sourav Ray (Fri Apr 24 2015 - 00:45:44 CDT)
  - RE: Which Binary to use? Norman Geist (Mon Apr 27 2015 - 01:59:17 CDT)
How to output CCC per residue from MDFF Michael Yuchi (Thu Apr 23 2015 - 21:48:11 CDT)
- Re: How to output CCC per residue from MDFF Ryan McGreevy (Thu Apr 23 2015 - 22:15:49 CDT)
How to save a structure after minimizing for 1000 steps? Arijit Ghosh (Thu Apr 23 2015 - 16:15:40 CDT)
- Re: How to save a structure after minimizing for 1000 steps? Aron Broom (Thu Apr 23 2015 - 16:28:47 CDT)
- Re: How to save a structure after minimizing for 1000 steps? Chitrak Gupta (Thu Apr 23 2015 - 16:35:58 CDT)
energy minimization in namd Hasan haska (Thu Apr 23 2015 - 11:29:43 CDT)
- Re: energy minimization in namd Chitrak Gupta (Thu Apr 23 2015 - 11:44:51 CDT)
  - Re: energy minimization in namd Branko (Thu Apr 23 2015 - 11:57:06 CDT)
- Re: energy minimization in namd Brian Radak (Thu Apr 23 2015 - 11:51:26 CDT)
Equilibration for a reverse FEP run Matthew Ralph Adendorff (Thu Apr 23 2015 - 09:54:41 CDT)
- Re: Equilibration for a reverse FEP run Chris Chipot (Thu Apr 23 2015 - 10:04:32 CDT)
  - RE: Equilibration for a reverse FEP run Matthew Ralph Adendorff (Thu Apr 23 2015 - 10:16:08 CDT)
restart simulation oguz gurbulak (Thu Apr 23 2015 - 09:22:38 CDT)
polarizable carbon nanotubes ibrahim khalil (Tue Apr 21 2015 - 11:00:36 CDT)
energy minimization Dhiraj Srivastava (Mon Apr 20 2015 - 21:57:55 CDT)
Calculating RMSF per residue Abir Ganguly (Mon Apr 20 2015 - 12:58:24 CDT)
- Re: Calculating RMSF per residue Aron Broom (Mon Apr 20 2015 - 15:59:23 CDT)
  - Re: Calculating RMSF per residue Abir Ganguly (Tue Apr 21 2015 - 02:58:40 CDT)
Mail reg Parameter file Vidhya Sankar (Mon Apr 20 2015 - 07:57:34 CDT)
- Re: Mail reg Parameter file Fotis Baltoumas (Mon Apr 20 2015 - 08:48:36 CDT)
TIP4P topology and parameter files oguz gurbulak (Sun Apr 19 2015 - 05:18:41 CDT)
slow heating of system Dhiraj Srivastava (Sun Apr 19 2015 - 00:55:58 CDT)
- Re: slow heating of system Maxim Belkin (Sun Apr 19 2015 - 04:08:03 CDT)
Calculation of PMF between protein domains NAMD Chola Regmi (Fri Apr 17 2015 - 17:26:03 CDT)
- Re: Calculation of PMF between protein domains NAMD Josh Vermaas (Fri Apr 17 2015 - 17:43:49 CDT)
  - Re: Calculation of PMF between protein domains NAMD Giacomo Fiorin (Fri Apr 17 2015 - 17:48:33 CDT)
    - Re: Calculation of PMF between protein domains NAMD Josh Vermaas (Fri Apr 17 2015 - 17:54:37 CDT)
  - Re: Calculation of PMF between protein domains NAMD Aron Broom (Fri Apr 17 2015 - 17:57:48 CDT)
    - Re: Calculation of PMF between protein domains NAMD Aron Broom (Fri Apr 17 2015 - 18:00:09 CDT)
- Re: Calculation of PMF between protein domains NAMD Jeff Comer (Fri Apr 17 2015 - 18:22:17 CDT)
  - Re: Calculation of PMF between protein domains NAMD Chola Regmi (Fri Apr 17 2015 - 18:50:25 CDT)
    - Re: Calculation of PMF between protein domains NAMD Chola Regmi (Wed May 13 2015 - 18:14:49 CDT)
Problems when running FEP for mutation ASP to GLY Yunhui Peng (Fri Apr 17 2015 - 13:53:03 CDT)
Running two molecule coarse-grained simulation Sourav Ray (Wed Apr 15 2015 - 05:39:18 CDT)
- Re: Running two molecule coarse-grained simulation Sourav Ray (Wed Apr 15 2015 - 05:51:29 CDT)
  - Re: Running two molecule coarse-grained simulation Sourav Ray (Wed Apr 15 2015 - 09:05:43 CDT)
CHARMM parameter file Fransiska Kurniawan (Wed Apr 15 2015 - 04:11:00 CDT)
Problems to parametrize molecules Evandro Semighini (Tue Apr 14 2015 - 15:30:03 CDT)
- RE: Problems to parametrize molecules Bennion, Brian (Tue Apr 14 2015 - 15:45:41 CDT)
  - Re: Problems to parametrize molecules Evandro Semighini (Tue Apr 14 2015 - 15:51:17 CDT)
    - RE: Problems to parametrize molecules Bennion, Brian (Tue Apr 14 2015 - 15:57:28 CDT)
  - RE: Problems to parametrize molecules Bennion, Brian (Wed Apr 15 2015 - 13:04:21 CDT)
- Re: Problems to parametrize molecules Mayne, Christopher G (Fri Apr 17 2015 - 11:16:16 CDT)
  - Re: Re: Problems to parametrize molecules Evandro Semighini (Sun Apr 19 2015 - 18:47:21 CDT)
bilayer simulation keeps crashing Chitrak Gupta (Tue Apr 14 2015 - 10:00:27 CDT)
NetworkView plugin for the non-namd trajectories James Starlight (Tue Apr 14 2015 - 09:34:57 CDT)
- Re: NetworkView plugin for the non-namd trajectories Vlad Cojocaru (Tue Apr 14 2015 - 10:13:47 CDT)
Re: REMD on GPU cluster Michael Feig (Tue Apr 14 2015 - 08:00:16 CDT)
- RE: REMD on GPU cluster Norman Geist (Tue Apr 14 2015 - 11:01:49 CDT)
strange behavior of ABF Danilo Di Maio (Tue Apr 14 2015 - 05:41:24 CDT)
- Re: strange behavior of ABF JÃ©rÃ´me HÃ©nin (Tue Apr 14 2015 - 07:06:47 CDT)
  - Re: strange behavior of ABF Danilo Di Maio (Tue Apr 14 2015 - 12:48:13 CDT)
REMD on GPU cluster Michael Feig (Mon Apr 13 2015 - 17:09:05 CDT)
- RE: REMD on GPU cluster Norman Geist (Tue Apr 14 2015 - 02:10:03 CDT)
Can't find documentation of known bug in NAMD 2.9 Klas Karis (Mon Apr 13 2015 - 12:02:25 CDT)
TIP4P water for MD Abhishek TYAGI (Mon Apr 13 2015 - 07:44:51 CDT)
Can NAMD simulation solve the problem of coordinate clash in a structural model? sunyeping (Sun Apr 12 2015 - 21:19:18 CDT)
- Re: Can NAMD simulation solve the problem of coordinate clash in a structural model? Tristan Croll (Fri Apr 17 2015 - 16:50:07 CDT)
Re: Can NAMD simulation solve the problem of coordinate clash in a structural model? sunyeping (Sun Apr 12 2015 - 21:18:30 CDT)
Trouble using the extForces parameters Duster, Adam (Sat Apr 11 2015 - 04:11:42 CDT)
- Re: Trouble using the extForces parameters David Hardy (Sat Apr 11 2015 - 12:05:49 CDT)
Reg: topology file amidated and acetylated disulfide bridged Cystine Akshay Bhatnagar (Fri Apr 10 2015 - 05:05:42 CDT)
Immediate Postdoctoral Position Opening Marawan Hussien (Thu Apr 09 2015 - 18:10:32 CDT)
- Immediate PhD Opening Computational Structural Biology Of Membrane Proteins Marawan Hussien (Thu Apr 09 2015 - 19:18:53 CDT)
timestep querry Abhishek TYAGI (Wed Apr 01 2015 - 10:28:12 CDT)
- Re: timestep querry Aron Broom (Wed Apr 01 2015 - 10:51:31 CDT)
  - Re: timestep querry Abhishek TYAGI (Wed Apr 01 2015 - 11:15:49 CDT)
    - Re: timestep querry Brian Radak (Thu Apr 02 2015 - 14:17:47 CDT)
    - Re: timestep querry Abhishek TYAGI (Thu Apr 02 2015 - 23:07:39 CDT)
Daily cron stalls running NAMD outputs Vlastimil ZÃma (Wed Apr 01 2015 - 03:04:26 CDT)
- Re: Daily cron stalls running NAMD outputs Vlastimil ZÃma (Wed Apr 01 2015 - 07:08:28 CDT)
  - Re: Daily cron stalls running NAMD outputs Vlastimil ZÃma (Wed Apr 08 2015 - 02:41:23 CDT)
    - Re: Daily cron stalls running NAMD outputs JÃ©rÃ´me HÃ©nin (Wed Apr 08 2015 - 03:16:22 CDT)
problem about namdstats.tcl Hasan haska (Wed Apr 01 2015 - 01:34:32 CDT)
Minimisation not converged Kevin C Chan (Wed Apr 01 2015 - 01:20:37 CDT)
- Re: Minimisation not converged JÃ©rÃ´me HÃ©nin (Wed Apr 01 2015 - 02:14:12 CDT)
  - Re: Minimisation not converged Kevin C Chan (Wed Apr 01 2015 - 22:26:19 CDT)
    - Re: Minimisation not converged JÃ©rÃ´me HÃ©nin (Thu Apr 02 2015 - 06:52:36 CDT)
Enerygy Minimization of a homology modelled structure in NAMD Arijit Ghosh (Tue Mar 31 2015 - 22:46:49 CDT)
- Re: Enerygy Minimization of a homology modelled structure in NAMD JÃ©rÃ´me HÃ©nin (Wed Apr 01 2015 - 02:07:59 CDT)
ABF with external electric field Bala subramanian (Tue Mar 31 2015 - 10:42:24 CDT)
- Re: ABF with external electric field Jeff Comer (Tue Mar 31 2015 - 11:41:35 CDT)
  - Re: ABF with external electric field Giacomo Fiorin (Tue Mar 31 2015 - 13:16:15 CDT)
Dipole Moment Watcher, Ibuprofen JAVAD NOROOZI (Tue Mar 31 2015 - 01:01:46 CDT)
- Re: Dipole Moment Watcher, Ibuprofen Branko (Tue Mar 31 2015 - 04:12:14 CDT)
Enerygy Minimization of a homology modelled structure in NAMD Arijit Ghosh (Mon Mar 30 2015 - 00:21:35 CDT)
Enerygy Minimization of a homology modelled structure in NAMD Arijit Ghosh (Sun Mar 29 2015 - 21:16:03 CDT)
pressure value Hasan haska (Sun Mar 29 2015 - 14:23:28 CDT)
- Re: pressure value Brian Radak (Sun Mar 29 2015 - 15:30:42 CDT)
  - Re: pressure value Jeff Comer (Sun Mar 29 2015 - 16:54:09 CDT)
angle between 2 vectors as collective variable Vlad Cojocaru (Thu Mar 26 2015 - 09:17:41 CDT)
- Re: angle between 2 vectors as collective variable Giacomo Fiorin (Thu Mar 26 2015 - 09:58:26 CDT)
  - Re: angle between 2 vectors as collective variable Vlad Cojocaru (Thu Mar 26 2015 - 10:03:36 CDT)
    - Re: angle between 2 vectors as collective variable Giacomo Fiorin (Thu Mar 26 2015 - 10:16:25 CDT)
    - Re: angle between 2 vectors as collective variable Vlad Cojocaru (Thu Mar 26 2015 - 11:04:09 CDT)
bond angle and dihedral values oguz gurbulak (Thu Mar 26 2015 - 03:55:03 CDT)
Fwd: FW: NAMD Brian Radak (Wed Mar 25 2015 - 11:35:27 CDT)
Parallelization of External Program Forces btreece_at_andrew.cmu.edu (Tue Mar 24 2015 - 18:49:26 CDT)
about hydrogen bond analysis Hasan haska (Tue Mar 24 2015 - 16:07:08 CDT)
- Re: about hydrogen bond analysis Mo Chen (Tue Mar 24 2015 - 16:19:37 CDT)
Announcement: â€˜Hands Onâ€™ Workshop on Computational Biophysics (Lake Tahoe, CA, Aug 3-7, 2015) Lela Vukovic (Tue Mar 24 2015 - 15:50:58 CDT)
GPU Programming workshop @ ICTP: deadline extended for participants not requiring visa and financial support Axel Kohlmeyer (Tue Mar 24 2015 - 14:17:40 CDT)
NAMD nightly build compilation Vlad Cojocaru (Tue Mar 24 2015 - 12:07:03 CDT)
- Re: NAMD nightly build compilation Vlad Cojocaru (Tue Mar 24 2015 - 12:51:47 CDT)
  - Re: NAMD nightly build compilation Vlad Cojocaru (Thu May 07 2015 - 08:40:00 CDT)
Re: NAMD Subbarao Kanchi (Tue Mar 24 2015 - 01:48:39 CDT)
Restraining angle between bond vector and coordinate vector Seth Axen (Mon Mar 23 2015 - 15:26:37 CDT)
- Re: Restraining angle between bond vector and coordinate vector JÃ©rÃ´me HÃ©nin (Mon Mar 23 2015 - 15:45:02 CDT)
- Re: Restraining angle between bond vector and coordinate vector Jeff Comer (Mon Mar 23 2015 - 18:17:18 CDT)
  - Re: Restraining angle between bond vector and coordinate vector Seth Axen (Wed Mar 25 2015 - 19:01:40 CDT)
Immediate Postdoctoral Position Opening Marawan Hussien (Sun Mar 22 2015 - 16:08:16 CDT)
number of close contacts and contact area Abhishek TYAGI (Sun Mar 22 2015 - 04:37:57 CDT)
error while running namd on CRAY XC40 machine Santosh Kumar Chaudhary (Sun Mar 22 2015 - 02:40:31 CDT)
- Re: error while running namd on CRAY XC40 machine Jim Phillips (Mon Mar 23 2015 - 13:59:47 CDT)
  - Re: error while running namd on CRAY XC40 machine Santosh Kumar Chaudhary (Fri Mar 27 2015 - 01:00:51 CDT)
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2 Sadegh Faramarzi Ganjabad (Wed Mar 18 2015 - 16:47:50 CDT)
- Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2 Jeff Comer (Wed Mar 18 2015 - 17:35:39 CDT)
  - Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2 Josh Vermaas (Wed Mar 18 2015 - 17:42:03 CDT)
  - Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OC2D2 Sadegh Faramarzi Ganjabad (Wed Mar 18 2015 - 17:50:58 CDT)
DCD Error Abhishek TYAGI (Wed Mar 18 2015 - 06:23:58 CDT)
- Re: DCD Error manish kesherwani (Wed Mar 18 2015 - 08:10:18 CDT)
- Re: DCD Error btreece_at_andrew.cmu.edu (Wed Mar 18 2015 - 09:27:28 CDT)
  - Re: DCD Error Abhishek Tyagi (Wed Mar 18 2015 - 09:29:42 CDT)
Reg: solvating in a non-standard solvent Akshay Bhatnagar (Wed Mar 18 2015 - 01:29:20 CDT)
- Re: Reg: solvating in a non-standard solvent Branko (Wed Mar 18 2015 - 07:19:45 CDT)
  - Re: Reg: solvating in a non-standard solvent Josh Vermaas (Wed Mar 18 2015 - 09:08:24 CDT)
- Re: Reg: solvating in a non-standard solvent Jeff Comer (Wed Mar 18 2015 - 09:44:12 CDT)
  - Re: Reg: solvating in a non-standard solvent Akshay Bhatnagar (Thu Mar 19 2015 - 01:40:55 CDT)
1-4scaling for glycosylated protein using AMBER/GLYCAM FF in NAMD clarkzhy (Tue Mar 17 2015 - 20:33:41 CDT)
- Re: 1-4scaling for glycosylated protein using AMBER/GLYCAM FF in NAMD Lachele Foley (Tue Mar 17 2015 - 21:15:41 CDT)
  - Re: Re: 1-4scaling for glycosylated protein using AMBER/GLYCAM FF in NAMD clarkzhy (Tue Mar 17 2015 - 21:18:48 CDT)
    - Re: Re: 1-4scaling for glycosylated protein using AMBER/GLYCAM FF in NAMD Lachele Foley (Tue Mar 17 2015 - 21:46:19 CDT)
Restarting an abruptly interrupted simulation Sourav Ray (Tue Mar 17 2015 - 01:30:21 CDT)
- Re: Restarting an abruptly interrupted simulation Prathit Chatterjee (Tue Mar 17 2015 - 02:03:52 CDT)
Truncated octahedron : Problems in PBC when reading a dcd file with NAMD Panel Nicolas (M.) (Mon Mar 16 2015 - 11:18:00 CDT)
Updated Link: Postdoc positions available at IBM (bio-molecular modeling and MD) Payel Das (Mon Mar 16 2015 - 10:50:46 CDT)
- Re: Updated Link: Postdoc positions available at IBM (bio-molecular modeling and MD) Sourav Ray (Mon Mar 16 2015 - 12:30:29 CDT)
Postdoc positions available at IBM (bio-molecular modeling and MD) Payel Das (Mon Mar 16 2015 - 09:15:05 CDT)
Re: Restarting NAMD simulation Sourav Ray (Thu Mar 12 2015 - 09:16:26 CDT)
RE: Restarting NAMD simulation Norman Geist (Thu Mar 12 2015 - 09:13:14 CDT)
Restarting NAMD simulation Sourav Ray (Thu Mar 12 2015 - 08:30:27 CDT)
PACE Force Field and NAMD 2.10 Fotis Baltoumas (Thu Mar 12 2015 - 06:18:07 CDT)
Colvar with variable axis Mitchell Gleed (Thu Mar 12 2015 - 06:01:56 CDT)
- Re: Colvar with variable axis Giacomo Fiorin (Thu Mar 12 2015 - 06:23:31 CDT)
  - Re: Colvar with variable axis Mitchell Gleed (Thu Mar 12 2015 - 07:59:56 CDT)
Dihedral calculation with colvars Kevin C Chan (Wed Mar 11 2015 - 23:05:45 CDT)
- Re: Dihedral calculation with colvars Aron Broom (Wed Mar 11 2015 - 23:17:09 CDT)
  - Re: Dihedral calculation with colvars Kevin C Chan (Thu Mar 12 2015 - 01:20:46 CDT)
  - Re: Dihedral calculation with colvars JÃ©rÃ´me HÃ©nin (Fri Mar 13 2015 - 09:42:21 CDT)
    - Re: Dihedral calculation with colvars Giacomo Fiorin (Fri Mar 13 2015 - 10:05:20 CDT)
problem restarting multiple walker metadynamics Amy Rice (Wed Mar 11 2015 - 14:59:46 CDT)
- Re: problem restarting multiple walker metadynamics Giacomo Fiorin (Wed Mar 11 2015 - 18:29:36 CDT)
  - Re: problem restarting multiple walker metadynamics Amy Rice (Wed Mar 11 2015 - 22:49:51 CDT)
vdw parameter error | atom type <-> name problem Art (Wed Mar 11 2015 - 14:03:38 CDT)
No steric clashes, still not minimizing Francesco Pietra (Wed Mar 11 2015 - 06:38:40 CDT)
- Fwd: No steric clashes, still not minimizing Francesco Pietra (Wed Mar 11 2015 - 12:28:44 CDT)
equilibrate the bulk water system Hasan haska (Tue Mar 10 2015 - 16:51:30 CDT)
- RE: equilibrate the bulk water system Norman Geist (Wed Mar 11 2015 - 02:03:46 CDT)
  - Re: equilibrate the bulk water system Hasan haska (Fri Mar 13 2015 - 06:57:15 CDT)
Dihedral definition in NAMD Kevin C Chan (Tue Mar 10 2015 - 06:19:16 CDT)
- Re: Dihedral definition in NAMD Giacomo Fiorin (Tue Mar 10 2015 - 06:28:26 CDT)
  - Re: Dihedral definition in NAMD Kevin C Chan (Tue Mar 10 2015 - 06:52:53 CDT)
Alchemical FEP calculation involving glycine jostmey . (Mon Mar 09 2015 - 23:58:31 CDT)
- Re: Alchemical FEP calculation involving glycine Chris Chipot (Tue Mar 10 2015 - 05:59:57 CDT)
  - Re: Alchemical FEP calculation involving glycine jostmey . (Wed Mar 11 2015 - 17:57:02 CDT)
    - Re: Alchemical FEP calculation involving glycine JÃ©rÃ´me HÃ©nin (Thu Mar 12 2015 - 04:26:18 CDT)
Topology and Parameter File Fransiska Kurniawan (Mon Mar 09 2015 - 01:52:36 CDT)
about langevin dynamics Gisella Alfonsino (Sun Mar 08 2015 - 05:36:28 CDT)
- RE: about langevin dynamics Norman Geist (Mon Mar 09 2015 - 01:44:18 CDT)
energy groups in NAMD Andre Ribeiro (Fri Mar 06 2015 - 14:22:34 CST)
energy groups in NAMD Andre Ribeiro (Fri Mar 06 2015 - 14:23:14 CST)
NAMD warning: Randomization of stack point is turned on in kernal, thread migration may not work! Yarrow Madrona (Thu Mar 05 2015 - 10:58:11 CST)
- Re: NAMD warning: Randomization of stack point is turned on in kernal, thread migration may not work! Axel Kohlmeyer (Thu Mar 05 2015 - 11:40:42 CST)
Announcement: â€˜Hands Onâ€™ Workshop on Computational Biophysics (Pittsburgh, PA, June 1-5, 2015) Lela Vukovic (Wed Mar 04 2015 - 13:07:25 CST)
BUG: NAMD-2.10 CUDA REMD segfault with TCL exec randomly Norman Geist (Wed Mar 04 2015 - 01:47:42 CST)
- RE: BUG: NAMD-2.10 CUDA REMD segfault with TCL exec randomly Norman Geist (Wed Mar 04 2015 - 04:40:07 CST)
"Unknown command-line option +replicas" Mitul Saha (Mon Mar 02 2015 - 23:33:11 CST)
- namd simulation Urszula Uciechowska (Tue Mar 03 2015 - 08:20:25 CST)
  - Re: namd simulation Abhishek TYAGI (Thu Mar 05 2015 - 04:46:29 CST)
- RE: "Unknown command-line option +replicas" Norman Geist (Tue Mar 03 2015 - 08:35:47 CST)
WHICH VERSION OF NAMD SHOULD I INSTALL ON MY SYSTEM? Amin Dehkharghani (Sun Mar 01 2015 - 14:58:08 CST)
- Re: WHICH VERSION OF NAMD SHOULD I INSTALL ON MY SYSTEM? Richard Overstreet (Sun Mar 01 2015 - 16:56:39 CST)
- Re: WHICH VERSION OF NAMD SHOULD I INSTALL ON MY SYSTEM? Jeff Comer (Mon Mar 02 2015 - 10:45:28 CST)
How to let NAMD terminate automatically at a given time ÂÀÇç (Fri Feb 27 2015 - 20:02:18 CST)
- Re: How to let NAMD terminate automatically at a given time Dong Luo (Mon Mar 02 2015 - 09:27:22 CST)
  - Re: How to let NAMD terminate automatically at a given time JÃ©rÃ´me HÃ©nin (Mon Mar 02 2015 - 11:12:40 CST)
accelMD and GBIS? Brian Radak (Fri Feb 27 2015 - 18:15:13 CST)
scaling non-bonded interactiion parameter for specific pairs MEHRAN MB (Fri Feb 27 2015 - 13:15:11 CST)
- Re: scaling non-bonded interactiion parameter for specific pairs Jeff Comer (Fri Feb 27 2015 - 13:58:31 CST)
  - Re: scaling non-bonded interactiion parameter for specific pairs MEHRAN MB (Fri Feb 27 2015 - 14:01:29 CST)
configuration file question Hasan haska (Thu Feb 26 2015 - 16:49:55 CST)
- Re: configuration file question Jeff Comer (Thu Feb 26 2015 - 17:34:09 CST)
velocity IO with psfgen? Brian Radak (Thu Feb 26 2015 - 09:41:04 CST)
- Re: vmd-l: velocity IO with psfgen? John Stone (Thu Feb 26 2015 - 10:24:36 CST)
- Re: velocity IO with psfgen? Ajasja LjubetiÄ (Thu Feb 26 2015 - 10:37:55 CST)
  - Re: velocity IO with psfgen? Brian Radak (Thu Feb 26 2015 - 10:56:57 CST)
Rotating Constraints Sourav Purohit (Tue Feb 24 2015 - 14:23:26 CST)
Questions about lambda scheme in free energy perturbation Jian Dai (Tue Feb 24 2015 - 08:59:57 CST)
- Re: Questions about lambda scheme in free energy perturbation JÃ©rÃ´me HÃ©nin (Tue Feb 24 2015 - 16:18:21 CST)
Aggregation related analysis scripts Aditya Ranganathan (Tue Feb 24 2015 - 02:28:10 CST)
- Re: Aggregation related analysis scripts JÃ©rÃ´me HÃ©nin (Tue Feb 24 2015 - 09:39:01 CST)
  - Re: Aggregation related analysis scripts Jeff Comer (Tue Feb 24 2015 - 15:39:12 CST)
    - Re: Aggregation related analysis scripts Aditya Ranganathan (Wed Feb 25 2015 - 01:13:42 CST)
Alchemical FEP calculations in Implicit Solvent jostmey . (Mon Feb 23 2015 - 13:04:15 CST)
- Re: Alchemical FEP calculations in Implicit Solvent MEHRAN MB (Mon Feb 23 2015 - 13:08:56 CST)
  - Re: Alchemical FEP calculations in Implicit Solvent jostmey . (Mon Feb 23 2015 - 13:21:57 CST)
    - Re: Alchemical FEP calculations in Implicit Solvent jostmey . (Mon Feb 23 2015 - 14:45:13 CST)
My Plight Syed Kashif Zafar (Wed Feb 18 2015 - 18:28:19 CST)
FATAL ERROR: Low global exclusion count! Yongcheng Zhou (Wed Feb 18 2015 - 18:29:33 CST)
- Re: FATAL ERROR: Low global exclusion count! Akshata Rudrapatna (Wed Feb 18 2015 - 18:32:03 CST)
- Re: FATAL ERROR: Low global exclusion count! Jeff Comer (Wed Feb 18 2015 - 18:59:28 CST)
GPU Multinodes problem horacio poblete (Wed Feb 18 2015 - 15:59:07 CST)
- Re: GPU Multinodes problem Jim Phillips (Wed Feb 18 2015 - 17:36:26 CST)
compile psfgen as shared object or Tcl package? Brian Radak (Wed Feb 18 2015 - 15:47:27 CST)
Multicore-CUDA NAMD output hangs Mitchell Gleed (Wed Feb 18 2015 - 15:12:21 CST)
- Re: Multicore-CUDA NAMD output hangs Mitchell Gleed (Tue Mar 03 2015 - 10:34:20 CST)
NAMD Source, Molecule.c , Mass Critaria JAVAD NOROOZI (Wed Feb 18 2015 - 12:55:25 CST)
Maximum limit for "run" parameter Mitul Saha (Tue Feb 17 2015 - 18:50:38 CST)
- Re: Maximum limit for "run" parameter Jim Phillips (Wed Feb 18 2015 - 17:10:36 CST)
- Re: Maximum limit for "run" parameter Axel Kohlmeyer (Wed Feb 18 2015 - 17:15:30 CST)
  - Re: Maximum limit for "run" parameter Jim Phillips (Wed Feb 18 2015 - 17:49:41 CST)
multiple thermostats in adaptive tempering Igaev, Maxim (Wed Feb 18 2015 - 11:20:52 CST)
Re: Incorrect atom count in binary file Mihaela Drenscko (Wed Feb 18 2015 - 07:34:15 CST)
Incorrect atom count in binary file Mihaela Drenscko (Tue Feb 17 2015 - 18:59:43 CST)
- RE: Incorrect atom count in binary file Norman Geist (Wed Feb 18 2015 - 03:13:52 CST)
making dipeptides with psfgen - CMAP terms? Brian Radak (Tue Feb 17 2015 - 09:42:59 CST)
- Re: making dipeptides with psfgen - CMAP terms? Brian Radak (Tue Feb 17 2015 - 12:06:54 CST)
  - Re: making dipeptides with psfgen - CMAP terms? Jim Phillips (Tue Feb 17 2015 - 13:53:04 CST)
    - Re: making dipeptides with psfgen - CMAP terms? Brian Radak (Tue Feb 17 2015 - 16:10:49 CST)
Putting multiple copies of peptide in a box Aditya Ranganathan (Tue Feb 17 2015 - 03:39:14 CST)
Announcement: "Hands-On" Workshop on Computational Biophysics in Urbana, IL (April 6-10,2015) Lela Vukovic (Mon Feb 16 2015 - 14:44:55 CST)
problem with equilibration of membrane-protein system Azadeh Alavi (Sat Feb 14 2015 - 05:35:59 CST)
Compressibility of Berendesen Barostat (Simulations Near Critical Point) JAVAD NOROOZI (Fri Feb 13 2015 - 00:37:42 CST)
PSF generated with PSFGEN [problem in CP2K] - Problem with CGenFF naming? Christian Jorgensen (Thu Feb 12 2015 - 10:16:00 CST)
- Re: PSF generated with PSFGEN [problem in CP2K] - Problem with CGenFF naming? Jim Phillips (Thu Feb 12 2015 - 12:32:42 CST)
  - Re: PSF generated with PSFGEN [problem in CP2K] - Problem with CGenFF naming? Christian Jorgensen (Thu Feb 12 2015 - 13:01:13 CST)
Grid forces visualisation Charan Thota (Wed Feb 11 2015 - 06:13:12 CST)
- Re: Grid forces visualisation Jeff Comer (Wed Feb 11 2015 - 08:16:41 CST)
GBIS in NAMD 2.10 CUDA with IMD Tristan Croll (Wed Feb 11 2015 - 04:18:11 CST)
- Re: vmd-l: GBIS in NAMD 2.10 CUDA with IMD John Stone (Wed Feb 11 2015 - 10:03:39 CST)
- Re: GBIS in NAMD 2.10 CUDA with IMD Jim Phillips (Wed Feb 11 2015 - 10:51:31 CST)
  - Re: GBIS in NAMD 2.10 CUDA with IMD Tristan Croll (Wed Feb 11 2015 - 15:09:11 CST)
LangevinPistonPeriod (Simulation Near Critical Point) JAVAD NOROOZI (Tue Feb 10 2015 - 03:15:23 CST)
- single strand DNA in hairpin conformation Urszula Uciechowska (Thu Feb 12 2015 - 03:14:55 CST)
New web server for setup of membrane simulation systems Chen, Po-chia (Sun Feb 08 2015 - 06:17:35 CST)
Spikes in the Energy Plot Viswanath Pasumarthi (Mon Feb 09 2015 - 02:26:08 CST)
namd-1: Simulation Terminating Early Akshata Rudrapatna (Sat Feb 07 2015 - 15:06:33 CST)
- RE: namd-1: Simulation Terminating Early Norman Geist (Mon Feb 09 2015 - 03:09:57 CST)
- Re: namd-1: Simulation Terminating Early Jim Phillips (Mon Feb 09 2015 - 13:33:09 CST)
  - Re: namd-1: Simulation Terminating Early Akshata Rudrapatna (Mon Feb 09 2015 - 20:54:55 CST)
Analysis plugins for Martini Coarse Grained protein simulations Aditya Ranganathan (Sat Feb 07 2015 - 03:55:33 CST)
- Re: Analysis plugins for Martini Coarse Grained protein simulations Fotis Baltoumas (Sat Feb 07 2015 - 05:25:50 CST)
Targeted MD and the MARTINI Coarse-Grained Force Field Fotis Baltoumas (Fri Feb 06 2015 - 10:06:55 CST)
preparing dsDNA Urszula Uciechowska (Fri Feb 06 2015 - 05:58:43 CST)
Residue number changed to hexadecimal string K Miura (Thu Feb 05 2015 - 23:34:24 CST)
- Re: Residue number changed to hexadecimal string Jim Phillips (Fri Feb 06 2015 - 00:38:00 CST)
on-the-fly parameter introspection Brian Radak (Thu Feb 05 2015 - 13:54:51 CST)
- Re: on-the-fly parameter introspection Jim Phillips (Mon Feb 09 2015 - 13:18:02 CST)
Editing Patch Grid Dimensions Ryan Gordon (Thu Feb 05 2015 - 10:00:28 CST)
- Re: Editing Patch Grid Dimensions Jim Phillips (Thu Feb 05 2015 - 10:32:28 CST)
  - Re: Editing Patch Grid Dimensions Ryan Gordon (Thu Feb 05 2015 - 12:08:20 CST)
(no subject) Ma'Mon Hatmal (Thu Feb 05 2015 - 06:32:09 CST)
- RE: Norman Geist (Thu Feb 05 2015 - 07:55:53 CST)
Could I run aMD in Drude force field? dream (Thu Feb 05 2015 - 02:14:04 CST)
- Re: Could I run aMD in Drude force field? Brian Radak (Thu Feb 05 2015 - 13:50:15 CST)
Extracting data Stephan Grein (Wed Feb 04 2015 - 05:55:37 CST)
- Re: Extracting data Stephan Grein (Wed Feb 04 2015 - 05:56:47 CST)
- Re: Extracting data Jeff Comer (Wed Feb 04 2015 - 07:56:42 CST)
  - Re: Extracting data Axel Kohlmeyer (Wed Feb 04 2015 - 08:24:25 CST)
    - Re: Extracting data Jeff Comer (Wed Feb 04 2015 - 08:39:33 CST)
    - Re: Extracting data Stephan Grein (Thu Feb 05 2015 - 03:44:29 CST)
Alchemy Shift Coefficient at Low Density Regime (TI) JAVAD NOROOZI (Wed Feb 04 2015 - 02:58:15 CST)
- Re: Alchemy Shift Coefficient at Low Density Regime (TI) Brian Radak (Thu Feb 05 2015 - 13:44:14 CST)
Phi vs GPU Francesco Pietra (Wed Feb 04 2015 - 01:52:43 CST)
Fwd: all atom equilibrium of yeast PGK simulation with NAMD Qing Li (Tue Feb 03 2015 - 21:14:36 CST)
namd simulation with TIP5P Shanshan Wu (Tue Feb 03 2015 - 18:36:34 CST)
- Re: namd simulation with TIP5P Monika Madhavi (Fri Oct 02 2015 - 01:16:41 CDT)
namd-1: Fatal Error: Unable to Open CHARMM Parameter File Akshata Rudrapatna (Tue Feb 03 2015 - 14:43:55 CST)
- Re: namd-1: Fatal Error: Unable to Open CHARMM Parameter File David Hardy (Tue Feb 03 2015 - 15:32:57 CST)
  - Re: namd-1: Fatal Error: Unable to Open CHARMM Parameter File David Hardy (Tue Feb 03 2015 - 15:54:49 CST)
    - namd-1: Fatal Error: Unable to Open CHARMM Parameter File Branko (Tue Feb 03 2015 - 16:14:32 CST)
- Re: namd-1: Fatal Error: Unable to Open CHARMM Parameter File Jim Phillips (Tue Feb 03 2015 - 18:48:35 CST)
  - Re: namd-1: Fatal Error: Unable to Open CHARMM Parameter File Akshata Rudrapatna (Thu Feb 05 2015 - 06:32:40 CST)
LAST CALL: Free Energy Workshop, MÃ¼nster, March 9-11, 2015 Vlad Cojocaru (Tue Feb 03 2015 - 14:34:42 CST)
Calculation of the water inside of protein during trajectory James Starlight (Tue Feb 03 2015 - 09:51:07 CST)
error running min Urszula Uciechowska (Tue Feb 03 2015 - 08:23:28 CST)
- Re: error running min Jeff Comer (Tue Feb 03 2015 - 08:32:57 CST)
Re: vmd-l: vmd-I: Fatal Error: Unable to Open CHARMM Parameter File Ajasja LjubetiÄ (Tue Feb 03 2015 - 07:06:43 CST)
adjust water box size in RBCG Yongcheng Zhou (Sun Feb 01 2015 - 16:03:54 CST)
Message about timing in *log file. Dawid das (Sun Feb 01 2015 - 05:05:39 CST)
- Re: Message about timing in *log file. Jim Phillips (Mon Feb 02 2015 - 00:15:09 CST)
NAMD 2.10 with multiple-replica support Branko (Sat Jan 31 2015 - 14:06:06 CST)
- Re: NAMD 2.10 with multiple-replica support Jim Phillips (Mon Feb 02 2015 - 00:11:26 CST)
LCPO parameters P1-P4 yandong Huang (Sat Jan 31 2015 - 13:24:55 CST)
LJcorrection and alchemy? Brian Radak (Fri Jan 30 2015 - 12:10:53 CST)
- Re: LJcorrection and alchemy? Brian Radak (Fri Jan 30 2015 - 14:15:01 CST)
Histidine C-H---O hydrogen bonding eprates_at_iqm.unicamp.br (Thu Jan 29 2015 - 09:03:17 CST)
- Re: Histidine C-H---O hydrogen bonding Josh Vermaas (Thu Jan 29 2015 - 09:21:27 CST)
  - Re: Histidine C-H---O hydrogen bonding eprates_at_iqm.unicamp.br (Thu Jan 29 2015 - 11:36:33 CST)
    - Re: Histidine C-H---O hydrogen bonding Tanner, John J. (Thu Jan 29 2015 - 12:51:42 CST)
  - Re: Histidine C-H---O hydrogen bonding eprates_at_iqm.unicamp.br (Thu Jan 29 2015 - 11:39:57 CST)
    - Re: Histidine C-H---O hydrogen bonding Branko (Thu Jan 29 2015 - 12:53:52 CST)
AW: problem with water molecules angle in MD simulation Norman Geist (Thu Jan 29 2015 - 01:56:18 CST)
- Re: problem with water molecules angle in MD simulation Tristan Croll (Fri Jan 30 2015 - 02:25:32 CST)
  - Re: problem with water molecules angle in MD simulation Shoresh Shafei (Fri Jan 30 2015 - 02:28:17 CST)
    - Re: problem with water molecules angle in MD simulation Tristan Croll (Fri Jan 30 2015 - 02:43:42 CST)
    - Re: problem with water molecules angle in MD simulation Axel Kohlmeyer (Fri Jan 30 2015 - 05:32:06 CST)
AW: problem with water molecules angle in MD simulation Norman Geist (Wed Jan 28 2015 - 10:50:47 CST)
Is it possible to rename atoms with psfgen? Brian Radak (Wed Jan 28 2015 - 09:54:16 CST)
- Re: Is it possible to rename atoms with psfgen? Jim Phillips (Thu Jan 29 2015 - 13:11:46 CST)
  - Re: Is it possible to rename atoms with psfgen? Brian Radak (Fri Jan 30 2015 - 10:35:43 CST)
inconsistency in ABF results for helix unfolding MEHRAN MB (Tue Jan 27 2015 - 17:09:19 CST)
- Re: inconsistency in ABF results for helix unfolding gmail (Wed Jan 28 2015 - 03:49:54 CST)
  - Re: inconsistency in ABF results for helix unfolding Ajasja LjubetiÄ (Wed Jan 28 2015 - 04:05:37 CST)
System unstable after turning electric field on. Dawid das (Tue Jan 27 2015 - 11:26:50 CST)
- Re: System unstable after turning electric field on. Jeff Comer (Tue Jan 27 2015 - 13:22:38 CST)
  - Re: System unstable after turning electric field on. Jeff Comer (Tue Jan 27 2015 - 14:04:26 CST)
Re: problem with water molecules angle in MD simulation Shoresh (Tue Jan 27 2015 - 10:30:54 CST)
- AW: problem with water molecules angle in MD simulation Norman Geist (Wed Jan 28 2015 - 04:08:53 CST)
AW: problem with water molecules angle in MD simulation Norman Geist (Tue Jan 27 2015 - 02:28:18 CST)
AW: about angles in coordination complexes Norman Geist (Tue Jan 27 2015 - 02:23:29 CST)
LCPO parameters P1-P4 yandong Huang (Mon Jan 26 2015 - 12:30:21 CST)
Re: about angles in coordination complexes luca belmonte (Mon Jan 26 2015 - 09:28:16 CST)
- Re: about angles in coordination complexes JÃ©rÃ´me HÃ©nin (Mon Jan 26 2015 - 09:56:07 CST)
  - Re: about angles in coordination complexes luca belmonte (Mon Jan 26 2015 - 10:02:27 CST)
- Re: about angles in coordination complexes luca belmonte (Wed Feb 04 2015 - 04:37:28 CST)
about angles in coordination complexes luca belmonte (Mon Jan 26 2015 - 08:39:17 CST)
- AW: about angles in coordination complexes Norman Geist (Mon Jan 26 2015 - 09:24:39 CST)
Re: problems compiling NAMD with mpicxx from mvapich2 Jose Borreguero (Mon Jan 26 2015 - 08:27:41 CST)
problem with water molecules angle in MD simulation Shoresh Shafei (Sun Jan 25 2015 - 19:06:23 CST)
- AW: problem with water molecules angle in MD simulation Norman Geist (Mon Jan 26 2015 - 02:43:41 CST)
PMEGridSize and parameters controlling electrostatic interactions. Dawid das (Sat Jan 24 2015 - 13:48:44 CST)
- Re: PMEGridSize and parameters controlling electrostatic interactions. Maxim Belkin (Sat Jan 24 2015 - 14:11:59 CST)
- Re: PMEGridSize and parameters controlling electrostatic interactions. Jeff Comer (Sun Jan 25 2015 - 18:11:17 CST)
  - Re: PMEGridSize and parameters controlling electrostatic interactions. Maxim Belkin (Sun Jan 25 2015 - 21:20:58 CST)
problems compiling NAMD with mpicxx from mvapich2 Jose Borreguero (Sat Jan 24 2015 - 11:49:02 CST)
- AW: problems compiling NAMD with mpicxx from mvapich2 Norman Geist (Mon Jan 26 2015 - 02:36:17 CST)
Hamiltonian Replica Exchange MD Simulation in NAMD Fidan Sumbul (Fri Jan 23 2015 - 13:04:19 CST)
- Re: Hamiltonian Replica Exchange MD Simulation in NAMD JC Gumbart (Tue Jan 27 2015 - 08:52:42 CST)
  - Re: Hamiltonian Replica Exchange MD Simulation in NAMD Fidan Sumbul (Tue Jan 27 2015 - 14:07:31 CST)
NAMD "unable to find improper parameters" Asma El-Magboub (Thu Jan 22 2015 - 21:32:09 CST)
about compiling NAMD using intel icc and impi XSC (Fri Jan 23 2015 - 04:00:29 CST)
- AW: about compiling NAMD using intel icc and impi Norman Geist (Fri Jan 23 2015 - 04:59:43 CST)
tclBCArgs, passing floating point lists btreece_at_andrew.cmu.edu (Thu Jan 22 2015 - 14:03:21 CST)
- Re: tclBCArgs, passing floating point lists Jim Phillips (Thu Jan 22 2015 - 14:27:15 CST)
Reverse osmosis simulation Z (Thu Jan 22 2015 - 05:09:24 CST)
Local minima on minimiztion with colvars Francesco Pietra (Wed Jan 21 2015 - 12:45:14 CST)
- Fwd: Local minima on minimiztion with colvars Francesco Pietra (Wed Jan 21 2015 - 13:01:33 CST)
  - Re: Fwd: Local minima on minimiztion with colvars Francesco Pietra (Thu Jan 22 2015 - 02:55:09 CST)
FEP Restart file g_at_ut#@m! (Wed Jan 21 2015 - 08:26:15 CST)
- Re: FEP Restart file JÃ©rÃ´me HÃ©nin (Wed Jan 21 2015 - 08:57:20 CST)
NAMD Non-features JAVAD NOROOZI (Wed Jan 21 2015 - 01:54:50 CST)
- Re: NAMD Non-features JÃ©rÃ´me HÃ©nin (Wed Jan 21 2015 - 04:38:17 CST)
  - Re: NAMD Non-features Axel Kohlmeyer (Wed Jan 21 2015 - 05:31:57 CST)
    - Re: NAMD Non-features Jeff Comer (Wed Jan 21 2015 - 09:35:27 CST)
- Re: NAMD Non-features Axel Kohlmeyer (Wed Jan 21 2015 - 05:24:41 CST)
  - Re: NAMD Non-features JAVAD NOROOZI (Wed Jan 21 2015 - 15:24:43 CST)
    - Re: NAMD Non-features Axel Kohlmeyer (Wed Jan 21 2015 - 15:54:49 CST)
Re: problems running amber parm7 Francesco Pietra (Tue Jan 20 2015 - 01:25:17 CST)
- AW: problems running amber parm7 Norman Geist (Tue Jan 20 2015 - 01:38:30 CST)
- Re: problems running amber parm7 Francesco Pietra (Tue Jan 20 2015 - 01:56:02 CST)
  - AW: problems running amber parm7 Norman Geist (Tue Jan 20 2015 - 02:10:44 CST)
Periodic Box Dimension (WrapAll is on) JAVAD NOROOZI (Mon Jan 19 2015 - 23:55:19 CST)
- AW: Periodic Box Dimension (WrapAll is on) Norman Geist (Tue Jan 20 2015 - 00:39:59 CST)
  - Re: AW: Periodic Box Dimension (WrapAll is on) JAVAD NOROOZI (Tue Jan 20 2015 - 01:37:18 CST)
    - AW: AW: Periodic Box Dimension (WrapAll is on) Norman Geist (Tue Jan 20 2015 - 02:07:47 CST)
problems running amber parm7 Francesco Pietra (Mon Jan 19 2015 - 13:03:44 CST)
- AW: problems running amber parm7 Norman Geist (Tue Jan 20 2015 - 00:19:40 CST)
Multiple Dihedral in CHARMM parameters JAVAD NOROOZI (Mon Jan 19 2015 - 01:19:37 CST)
- Re: Multiple Dihedral in CHARMM parameters JÃ©rÃ´me HÃ©nin (Mon Jan 19 2015 - 04:57:07 CST)
dual-boost aMD and the dV value in the output file Ozge Sensoy (Sun Jan 18 2015 - 14:00:47 CST)
Steered NAMD using AMBER Forcefield [Config File] Zeinab Emami (Sun Jan 18 2015 - 10:07:51 CST)
using NAMD with CHARMM36 ff Maria Bykhovskaia (Sat Jan 17 2015 - 19:26:29 CST)
- Re: using NAMD with CHARMM36 ff JC Gumbart (Sat Jan 17 2015 - 19:36:55 CST)
  - Re: using NAMD with CHARMM36 ff JC Gumbart (Sun Jan 18 2015 - 12:32:35 CST)
- Re: using NAMD with CHARMM36 ff Branko (Sun Jan 18 2015 - 11:46:38 CST)
  - Re: using NAMD with CHARMM36 ff Tristan Croll (Wed Jan 21 2015 - 01:37:05 CST)
Restart heating Francesco Pietra (Fri Jan 16 2015 - 12:04:33 CST)
- Re: Restart heating Fotis Baltoumas (Fri Jan 16 2015 - 12:26:09 CST)
NAMD 2.10 with MVAPICH2-GDR? David Chin (Thu Jan 15 2015 - 08:41:04 CST)
- Re: NAMD 2.10 with MVAPICH2-GDR? Jim Phillips (Fri Jan 16 2015 - 16:54:35 CST)
colvars: keyword "name" is not supported, or not recognized in this context. Francesco Pietra (Thu Jan 15 2015 - 09:52:16 CST)
- Fwd: colvars: keyword "name" is not supported, or not recognized in this context. Francesco Pietra (Thu Jan 15 2015 - 10:10:14 CST)
  - Re: Fwd: colvars: keyword "name" is not supported, or not recognized in this context. JÃ©rÃ´me HÃ©nin (Thu Jan 15 2015 - 10:34:22 CST)
    - Re: Fwd: colvars: keyword "name" is not supported, or not recognized in this context. Francesco Pietra (Thu Jan 15 2015 - 10:54:47 CST)
Running CUDA on a laptop Tristan Croll (Tue Jan 13 2015 - 18:29:59 CST)
- Re: Running CUDA on a laptop Tristan Croll (Tue Jan 13 2015 - 19:14:31 CST)
colvars and drude don't play nice? JC Gumbart (Tue Jan 13 2015 - 18:08:42 CST)
- Re: colvars and drude don't play nice? Giacomo Fiorin (Tue Jan 13 2015 - 18:31:38 CST)
  - Re: colvars and drude don't play nice? JC Gumbart (Wed Jan 14 2015 - 09:58:28 CST)
namd-I: How to assume the thickness of membrane when applying external Electric field ? Vy Phan (Tue Jan 13 2015 - 00:20:31 CST)
- Re: namd-I: How to assume the thickness of membrane when applying external Electric field ? Axel Kohlmeyer (Tue Jan 13 2015 - 07:21:49 CST)
  - Re: namd-I: How to assume the thickness of membrane when applying external Electric field ? Adelman, Joshua Lev (Tue Jan 13 2015 - 08:36:01 CST)
NAMD slows at startup phase 1 smp problem Ryan Gordon (Mon Jan 12 2015 - 12:24:31 CST)
- AW: NAMD slows at startup phase 1 smp problem Norman Geist (Tue Jan 13 2015 - 01:22:03 CST)
  - AW: NAMD slows at startup phase 1 smp problem Norman Geist (Tue Jan 13 2015 - 05:50:39 CST)
  - AW: NAMD slows at startup phase 1 smp problem Norman Geist (Tue Jan 13 2015 - 05:52:43 CST)
- Re: NAMD slows at startup phase 1 smp problem Jim Phillips (Wed Jan 14 2015 - 17:16:19 CST)
  - Re: NAMD slows at startup phase 1 smp problem Alexander Tzanov (Thu Jan 15 2015 - 10:05:16 CST)
    - Re: NAMD slows at startup phase 1 smp problem Jim Phillips (Thu Jan 15 2015 - 14:20:58 CST)
Reg. restarting a Thermodynamic Integration Run Aditya Chattopadhyay (Mon Jan 12 2015 - 09:32:26 CST)
Re: is there a method equivalent to conformational flooding in NAMD 2.10 Thomas Evangelidis (Mon Jan 12 2015 - 04:32:17 CST)
- Re: is there a method equivalent to conformational flooding in NAMD 2.10 JÃ©rÃ´me HÃ©nin (Mon Jan 12 2015 - 04:44:58 CST)
Multiple Tcouple JAVAD NOROOZI (Mon Jan 12 2015 - 03:35:01 CST)
is there a method equivalent to conformational flooding in NAMD 2.10 Thomas Evangelidis (Sun Jan 11 2015 - 07:43:36 CST)
- AW: is there a method equivalent to conformational flooding in NAMD 2.10 Norman Geist (Mon Jan 12 2015 - 00:53:25 CST)
Getting residue mapping correpond to bead using SBCG (Shape based CG) Model in Coarse Grain Builder VMD Christian Bope Domilongo (Fri Jan 09 2015 - 04:31:44 CST)
- Re: Getting residue mapping correpond to bead using SBCG (Shape based CG) Model in Coarse Grain Builder VMD Jeff Comer (Fri Jan 09 2015 - 08:23:03 CST)
  - Re: Getting residue mapping correpond to bead using SBCG (Shape based CG) Model in Coarse Grain Builder VMD Christian Bope Domilongo (Fri Jan 09 2015 - 09:18:32 CST)
Free Energy Workshop, MÃ¼nster, March 9-11, 2015 Vlad Cojocaru (Fri Jan 09 2015 - 03:19:04 CST)
Re: Failure MD with par7/rst7 amber input Francesco Pietra (Fri Jan 09 2015 - 02:31:55 CST)
Tempreture Profile along z axis JAVAD NOROOZI (Thu Jan 08 2015 - 03:23:12 CST)
- Re: Tempreture Profile along z axis Jim Phillips (Thu Jan 08 2015 - 10:48:58 CST)
  - AW: Tempreture Profile along z axis Norman Geist (Fri Jan 09 2015 - 02:23:04 CST)
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS Mihaela Drenscko (Wed Jan 07 2015 - 19:58:27 CST)
- Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS Jeff Comer (Wed Jan 07 2015 - 20:15:30 CST)
Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Wed Jan 07 2015 - 12:30:35 CST)
Using colvars for biasing potential in Umbrella Sampling begÃ¼m alaybeyoÄŸlu (Wed Jan 07 2015 - 10:01:17 CST)
- Re: Using colvars for biasing potential in Umbrella Sampling Giacomo Fiorin (Wed Jan 07 2015 - 10:08:11 CST)
Failure MD with par7/rst7 amber input Francesco Pietra (Wed Jan 07 2015 - 02:55:16 CST)
- AW: Failure MD with par7/rst7 amber input Norman Geist (Wed Jan 07 2015 - 03:28:15 CST)
Problem with Kinetic Energy of Atomselection JAVAD NOROOZI (Wed Jan 07 2015 - 00:53:38 CST)
topology & force field parameters for Sorbitan monooleate (span 80) Madhusoodanan M.R (Tue Jan 06 2015 - 20:32:39 CST)
Probelm with Lone Pairs on TIP4 model JAVAD NOROOZI (Tue Jan 06 2015 - 04:07:23 CST)
- AW: Probelm with Lone Pairs on TIP4 model Norman Geist (Tue Jan 06 2015 - 05:34:59 CST)
FEP, big variations in dG within a window Jonasson Gabriella (Mon Jan 05 2015 - 09:44:31 CST)
- Re: FEP, big variations in dG within a window Felipe Merino (Mon Jan 05 2015 - 10:27:30 CST)
Re: Temperature assignment REMD Yan Zhou (Mon Jan 05 2015 - 02:27:56 CST)
AW: error parsing config file while executing Norman Geist (Mon Jan 05 2015 - 00:26:37 CST)
regarding PME grid setting problem amit banerjee (Sun Jan 04 2015 - 18:31:44 CST)
- AW: regarding PME grid setting problem Norman Geist (Mon Jan 05 2015 - 00:48:11 CST)
Temperature assignment REMD divya nayar (Sat Jan 03 2015 - 08:36:05 CST)
- AW: Temperature assignment REMD Norman Geist (Mon Jan 05 2015 - 01:29:55 CST)
Reg: simulating an amino acid in dichloromethane Akshay Bhatnagar (Fri Jan 02 2015 - 23:18:45 CST)
- Re: Reg: simulating an amino acid in dichloromethane Jeff Comer (Sat Jan 03 2015 - 00:34:17 CST)
- Re: Reg: simulating an amino acid in dichloromethane Branko (Mon Jan 05 2015 - 05:39:13 CST)
  - Re: Reg: simulating an amino acid in dichloromethane Akshay Bhatnagar (Mon Jan 05 2015 - 06:46:07 CST)
    - Multiple tcouple (Nonequilbirium molecular dynamics) JAVAD NOROOZI (Tue Jan 06 2015 - 03:51:07 CST)
angles between residues luca belmonte (Tue Dec 30 2014 - 07:38:14 CST)
Lone Pair on H2S JAVAD NOROOZI (Tue Dec 30 2014 - 06:05:39 CST)
Lone Pair on H2S JAVAD NOROOZI (Tue Dec 30 2014 - 06:05:40 CST)
Lone Pair on H2S JAVAD NOROOZI (Sat Dec 27 2014 - 09:42:25 CST)
warnings while using amber files amin_at_imtech.res.in (Thu Dec 25 2014 - 05:14:20 CST)
- Re: warnings while using amber files amin_at_imtech.res.in (Thu Dec 25 2014 - 21:54:38 CST)
  - AW: warnings while using amber files Norman Geist (Mon Jan 05 2015 - 00:42:51 CST)
NAMD 2.10b1: occasional corrupted frame in binary dcd output Tristan Croll (Tue Dec 23 2014 - 16:39:46 CST)
Cannot find colvar dih1 (dih colvars) Francesco Pietra (Tue Dec 23 2014 - 11:15:31 CST)
- Fwd: Cannot find colvar dih1 (dih colvars) Francesco Pietra (Tue Dec 23 2014 - 14:23:04 CST)
  - Fwd: Cannot find colvar dih1 (dih colvars) Francesco Pietra (Tue Dec 23 2014 - 15:01:39 CST)
Error on write to binary file Mihaela Drenscko (Mon Dec 22 2014 - 18:02:54 CST)
- AW: Error on write to binary file Norman Geist (Tue Dec 23 2014 - 02:42:04 CST)
.inpcrd to .pdb Shalton Evans (Sun Dec 21 2014 - 13:56:30 CST)
- Re: .inpcrd to .pdb Jason Swails (Sun Dec 21 2014 - 20:04:39 CST)
Free Energy Workshop, Münster, March 9-11Q_2015?= Vlad Cojocaru (Fri Dec 19 2014 - 12:02:00 CST)
Re: FATAL ERROR: seek failed while writing DCD file: No such file or directory Douglas Houston (Fri Dec 19 2014 - 08:33:31 CST)
problem in installation of charm-6.4.0 in bluegeneL] Santosh Kumar Chaudhary (Fri Dec 19 2014 - 05:49:45 CST)
FATAL ERROR: seek failed while writing DCD file: No such file or directory Douglas Houston (Thu Dec 18 2014 - 14:39:51 CST)
- AW: FATAL ERROR: seek failed while writing DCD file: No such file or directory Norman Geist (Fri Dec 19 2014 - 00:35:26 CST)
  - Re: AW: FATAL ERROR: seek failed while writing DCD file: No such file or directory Douglas Houston (Fri Dec 19 2014 - 02:12:48 CST)
    - Re: AW: FATAL ERROR: seek failed while writing DCD file: No such file or directory Maxime Boissonneault (Fri Dec 19 2014 - 08:18:38 CST)
    - Re: AW: FATAL ERROR: seek failed while writing DCD file: No such file or directory Douglas Houston (Fri Dec 19 2014 - 08:40:04 CST)
Re: Asking help on results of our GPU benchmark å‘¨æ–‡æ˜Œ (Thu Dec 18 2014 - 13:24:59 CST)
- AW: Asking help on results of our GPU benchmark Norman Geist (Fri Dec 19 2014 - 00:30:22 CST)
- Re: Asking help on results of our GPU benchmark å‘¨æ–‡æ˜Œ (Fri Dec 19 2014 - 16:06:33 CST)
  - AW: Asking help on results of our GPU benchmark Norman Geist (Mon Dec 22 2014 - 01:16:12 CST)
- Re: Asking help on results of our GPU benchmark å‘¨æ–‡æ˜Œ (Mon Dec 22 2014 - 12:11:18 CST)
  - AW: Asking help on results of our GPU benchmark Norman Geist (Tue Dec 23 2014 - 02:34:58 CST)
- Re: Asking help on results of our GPU benchmark å‘¨æ–‡æ˜Œ (Tue Dec 23 2014 - 14:05:30 CST)
  - AW: Asking help on results of our GPU benchmark Norman Geist (Mon Jan 05 2015 - 00:37:40 CST)
- Re: Asking help on results of our GPU benchmark Axel Kohlmeyer (Mon Jan 05 2015 - 10:36:24 CST)
Re: Constant Pressure, Variable Volume, Minimization Miss. State (Thu Dec 18 2014 - 13:01:05 CST)
- Re: Re: Constant Pressure, Variable Volume, Minimization Josh Vermaas (Thu Dec 18 2014 - 13:17:35 CST)
Asking help on results of our GPU benchmark å‘¨æ–‡æ˜Œ (Wed Dec 17 2014 - 15:13:24 CST)
- AW: Asking help on results of our GPU benchmark Norman Geist (Thu Dec 18 2014 - 02:39:51 CST)
Loading Velocity DCD file JAVAD NOROOZI (Wed Dec 17 2014 - 13:23:20 CST)
- AW: Loading Velocity DCD file Norman Geist (Thu Dec 18 2014 - 02:31:16 CST)
Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Wed Dec 17 2014 - 10:24:50 CST)
setting up namd simulation in IBM Blue Gene/L Santosh Kumar Chaudhary (Wed Dec 17 2014 - 06:21:17 CST)
- RE: setting up namd simulation in IBM Blue Gene/L hannes.loeffler_at_stfc.ac.uk (Wed Dec 17 2014 - 07:07:23 CST)
  - RE: setting up namd simulation in IBM Blue Gene/L Santosh Kumar Chaudhary (Thu Dec 18 2014 - 00:09:48 CST)
    - RE: setting up namd simulation in IBM Blue Gene/L hannes.loeffler_at_stfc.ac.uk (Thu Dec 18 2014 - 01:36:36 CST)
    - RE: setting up namd simulation in IBM Blue Gene/L hannes.loeffler_at_stfc.ac.uk (Thu Dec 18 2014 - 01:43:11 CST)
- Re: setting up namd simulation in IBM Blue Gene/L Jim Phillips (Fri Dec 19 2014 - 12:55:33 CST)
  - Re: setting up namd simulation in IBM Blue Gene/L Santosh Kumar Chaudhary (Sat Dec 20 2014 - 01:53:14 CST)
Implementing the Virtual Bond Algorithm Using Colvars David Huggins (Wed Dec 17 2014 - 06:25:33 CST)
- Re: Implementing the Virtual Bond Algorithm Using Colvars Giacomo Fiorin (Thu Dec 18 2014 - 19:37:06 CST)
Extracting Kinetic Energy of Certain Atoms JAVAD NOROOZI (Wed Dec 17 2014 - 03:19:09 CST)
Is it so different when setting reinitvels or not? Zhao Lina (Wed Dec 17 2014 - 00:03:25 CST)
- Re: Is it so different when setting reinitvels or not? Jeff Comer (Wed Dec 17 2014 - 05:45:09 CST)
  - Re: Is it so different when setting reinitvels or not? Zhao Lina (Wed Dec 17 2014 - 19:31:49 CST)
Transferring bond list to new molecule Mert GÃ¼r (Tue Dec 16 2014 - 23:17:02 CST)
- Re: Transferring bond list to new molecule Josh Vermaas (Wed Dec 17 2014 - 08:18:18 CST)
  - Re: Transferring bond list to new molecule Mert GÃ¼r (Wed Dec 17 2014 - 18:06:05 CST)
Running Charmrun/NAMD with more than 10 processes fails K Miura (Tue Dec 16 2014 - 02:53:36 CST)
- AW: Running Charmrun/NAMD with more than 10 processes fails Norman Geist (Tue Dec 16 2014 - 04:06:49 CST)
Inspiration for most efficient implementation of coarse grained forcefield. Ajasja LjubetiÄ (Mon Dec 15 2014 - 12:08:03 CST)
- Re: Inspiration for most efficient implementation of coarse grained forcefield. JÃ©rÃ´me HÃ©nin (Mon Dec 15 2014 - 15:41:22 CST)
- Re: Inspiration for most efficient implementation of coarse grained forcefield. Jim Phillips (Tue Dec 16 2014 - 09:30:40 CST)
Error compiling NAMD2.9 after patching with PLUMED2.1 RubÃ©n Granero (Mon Dec 15 2014 - 06:47:27 CST)
- Re: Error compiling NAMD2.9 after patching with PLUMED2.1 Jim Phillips (Mon Dec 15 2014 - 08:37:26 CST)
  - Re: Error compiling NAMD2.9 after patching with PLUMED2.1 RubÃ©n Granero (Tue Dec 16 2014 - 07:39:02 CST)
    - Re: Error compiling NAMD2.9 after patching with PLUMED2.1 Jim Phillips (Tue Dec 16 2014 - 09:22:04 CST)
    - Re: Error compiling NAMD2.9 after patching with PLUMED2.1 RubÃ©n Granero (Tue Dec 16 2014 - 12:07:45 CST)
NAMD 2.10 released Jim Phillips (Fri Dec 12 2014 - 16:35:38 CST)
Info: Pairlistdist is too small for 3 computes during timestep 115001 Santosh Kumar Chaudhary (Fri Dec 12 2014 - 10:34:41 CST)
- Re: Info: Pairlistdist is too small for 3 computes during timestep 115001 Jim Phillips (Fri Dec 12 2014 - 15:49:06 CST)
- Re: Info: Pairlistdist is too small for 3 computes during timestep 115001 Subbarao Kanchi (Fri Dec 12 2014 - 16:26:26 CST)
question about FEP for amphiphile in lipid bilayer Leonardo Darre (Wed Dec 10 2014 - 08:08:27 CST)
- Re: question about FEP for amphiphile in lipid bilayer Giacomo Fiorin (Wed Dec 10 2014 - 08:41:25 CST)
  - Re: question about FEP for amphiphile in lipid bilayer Leonardo Darre (Wed Dec 10 2014 - 09:20:51 CST)
the difference of PCA and EDA ÂÀÐ¡Ó¨ (Wed Dec 10 2014 - 02:31:30 CST)
- Re: the difference of PCA and EDA Fotis Baltoumas (Wed Dec 10 2014 - 05:36:43 CST)
  - Re: the difference of PCA and EDA Hannes Loeffler (Wed Dec 10 2014 - 05:59:37 CST)
Empirical force fields: release of R.E.D. Server Dev./PyRED Nov. 2014 FyD (Tue Dec 09 2014 - 02:43:22 CST)
Choosing of windows and width for Umbrella Sampling Kevin C Chan (Mon Dec 08 2014 - 06:48:19 CST)
- Re: Choosing of windows and width for Umbrella Sampling Giacomo Fiorin (Mon Dec 08 2014 - 08:29:49 CST)
  - Re: Choosing of windows and width for Umbrella Sampling Kevin C Chan (Mon Dec 08 2014 - 09:39:46 CST)
query about the cross term in psf Kshatresh Dutta Dubey (Sat Dec 06 2014 - 13:31:42 CST)
- Re: query about the cross term in psf Josh Vermaas (Sat Dec 06 2014 - 13:49:06 CST)
  - Re: query about the cross term in psf Kshatresh Dutta Dubey (Sat Dec 06 2014 - 14:12:31 CST)
    - Re: query about the cross term in psf Josh Vermaas (Sat Dec 06 2014 - 14:22:32 CST)
colvars angle centerReference Jeff Comer (Fri Dec 05 2014 - 15:00:44 CST)
- Re: colvars angle centerReference Giacomo Fiorin (Tue Dec 09 2014 - 18:35:22 CST)
  - Re: colvars angle centerReference Jeff Comer (Tue Dec 09 2014 - 21:41:26 CST)
information about simulation speed Kshatresh Dutta Dubey (Tue Dec 02 2014 - 16:50:11 CST)
- Re: information about simulation speed Axel Kohlmeyer (Tue Dec 02 2014 - 16:53:44 CST)
  - Re: information about simulation speed Kshatresh Dutta Dubey (Tue Dec 02 2014 - 17:04:31 CST)
Running CUDA-enabled NAMD on multiple nodes without InfiniBand? Michel van der List (Mon Dec 01 2014 - 08:40:46 CST)
- AW: Running CUDA-enabled NAMD on multiple nodes without InfiniBand? Norman Geist (Mon Dec 01 2014 - 09:19:24 CST)
  - RE: Running CUDA-enabled NAMD on multiple nodes without InfiniBand? Michel van der List (Wed Dec 03 2014 - 12:06:03 CST)
    - AW: Running CUDA-enabled NAMD on multiple nodes without InfiniBand? Norman Geist (Thu Dec 04 2014 - 01:08:09 CST)
question about CUDA-enabled maryam atabay (Sat Nov 29 2014 - 10:19:49 CST)
- Re: question about CUDA-enabled Abhishek Tyagi (Sat Nov 29 2014 - 11:04:55 CST)
  - Re: question about CUDA-enabled Abhishek TYAGI (Sun Nov 30 2014 - 02:57:53 CST)
    - AW: question about CUDA-enabled Norman Geist (Mon Dec 01 2014 - 02:05:20 CST)
    - AW: question about CUDA-enabled Norman Geist (Mon Dec 01 2014 - 02:56:08 CST)
- Re: question about CUDA-enabled Axel Kohlmeyer (Sat Nov 29 2014 - 19:22:55 CST)
running NAMD in parallel Kshatresh Dutta Dubey (Fri Nov 28 2014 - 19:29:43 CST)
- Re: running NAMD in parallel Jim Phillips (Sat Nov 29 2014 - 16:51:06 CST)
Re: anisotropic pressure control Maxim Igaev (Wed Nov 26 2014 - 04:04:49 CST)
- AW: anisotropic pressure control Norman Geist (Wed Nov 26 2014 - 05:04:20 CST)
  - Re: anisotropic pressure control Maxim Igaev (Wed Nov 26 2014 - 05:10:09 CST)
Fw: anisotropic pressure control Maxim Igaev (Wed Nov 26 2014 - 03:47:41 CST)
anisotropic pressure control Maxim Igaev (Wed Nov 26 2014 - 02:48:51 CST)
- AW: anisotropic pressure control Norman Geist (Wed Nov 26 2014 - 03:22:31 CST)
colvar DistanceZ Kevin C Chan (Tue Nov 25 2014 - 21:03:55 CST)
- Re: colvar DistanceZ JÃ©rÃ´me HÃ©nin (Wed Nov 26 2014 - 05:07:19 CST)
  - Re: colvar DistanceZ Kevin C Chan (Wed Nov 26 2014 - 07:25:03 CST)
    - Re: colvar DistanceZ JÃ©rÃ´me HÃ©nin (Wed Nov 26 2014 - 07:35:37 CST)
    - Re: colvar DistanceZ Kevin C Chan (Wed Nov 26 2014 - 20:32:24 CST)
(no subject) flavio seixas (Tue Nov 25 2014 - 19:13:24 CST)
- AW: Norman Geist (Wed Nov 26 2014 - 02:26:35 CST)
  - Re: AW: flavio seixas (Wed Nov 26 2014 - 09:53:23 CST)
- (no subject) tillmann.utesch_at_mailbox.tu-berlin.de (Wed Nov 26 2014 - 03:20:51 CST)
question about CUDA-enabled maryam atabay (Tue Nov 25 2014 - 01:05:32 CST)
Colvars error Kevin C Chan (Tue Nov 25 2014 - 00:10:05 CST)
- Re: Colvars error Kevin C Chan (Tue Nov 25 2014 - 00:57:45 CST)
- Re: Colvars error Subbarao Kanchi (Tue Nov 25 2014 - 02:08:45 CST)
  - Re: Colvars error Kevin C Chan (Tue Nov 25 2014 - 05:11:55 CST)
    - Re: Colvars error Subbarao Kanchi (Tue Nov 25 2014 - 06:30:36 CST)
- Re: Colvars error Giacomo Fiorin (Tue Nov 25 2014 - 08:53:58 CST)
  - Re: Colvars error Kevin C Chan (Tue Nov 25 2014 - 21:11:41 CST)
"BAK" format files Ramin Ekhteiari (Mon Nov 24 2014 - 06:52:20 CST)
Fwd: question about CUDA-enabled maryam atabay (Mon Nov 24 2014 - 05:08:04 CST)
CGenFF atom type N- Francesco Pietra (Mon Nov 24 2014 - 02:55:04 CST)
Misleading failure of VMD with charge/CGenFF from waterbox Francesco Pietra (Sun Nov 23 2014 - 03:21:38 CST)
Fwd: Fwd: vmd-l: Re: problems with in text mode towards pdf and pdb files Francesco Pietra (Sat Nov 22 2014 - 02:45:10 CST)
11/22/2014 6:32:52 PM jeremy adler (Sat Nov 22 2014 - 00:32:52 CST)
A problem in ABF simulations Azadeh Alavi (Sat Nov 22 2014 - 05:50:03 CST)
- Re: A problem in ABF simulations Jeff Comer (Mon Nov 24 2014 - 11:44:45 CST)
tilt colvar JC Gumbart (Fri Nov 21 2014 - 11:09:55 CST)
- Re: tilt colvar Giacomo Fiorin (Fri Nov 21 2014 - 11:35:25 CST)
  - Re: tilt colvar JC Gumbart (Fri Nov 21 2014 - 18:12:31 CST)
  - Re: tilt colvar JC Gumbart (Tue Dec 02 2014 - 18:30:22 CST)
problems with in text mode towards pdf and pdb files Francesco Pietra (Fri Nov 21 2014 - 09:09:52 CST)
- Re: problems with in text mode towards pdf and pdb files Jim Phillips (Fri Nov 21 2014 - 09:29:35 CST)
  - Re: problems with in text mode towards pdf and pdb files Francesco Pietra (Fri Nov 21 2014 - 09:39:56 CST)
create psf file without hydrogens Revthi Sanker (Thu Nov 20 2014 - 12:26:48 CST)
- Re: create psf file without hydrogens Tristan Croll (Thu Nov 20 2014 - 14:22:06 CST)
  - Re: create psf file without hydrogens Revthi Sanker (Fri Nov 21 2014 - 03:23:19 CST)
carboxyl NBFIX on proteins Jeff Comer (Thu Nov 20 2014 - 09:18:45 CST)
- Re: carboxyl NBFIX on proteins Giacomo Fiorin (Thu Nov 20 2014 - 10:05:10 CST)
  - Re: carboxyl NBFIX on proteins Jeff Comer (Thu Nov 20 2014 - 10:46:35 CST)
about the vdw Interpolation calculation in NAMD source code Â¬Óíï¿ (Thu Nov 20 2014 - 02:44:40 CST)
- Re: about the vdw Interpolation calculation in NAMD source code Jeff Comer (Thu Nov 20 2014 - 08:20:54 CST)
- Re: about the vdw Interpolation calculation in NAMD source code Jim Phillips (Thu Nov 20 2014 - 08:29:27 CST)
  - Re: Re: about the vdw Interpolation calculation in NAMD source code Â¬Óíï¿ (Thu Nov 20 2014 - 09:32:10 CST)
    - Re: Re: about the vdw Interpolation calculation in NAMD source code Jim Phillips (Thu Nov 20 2014 - 16:00:29 CST)
    - Re: Re: Re: about the vdw Interpolation calculation in NAMD source code Â¬Óíï¿ (Thu Nov 20 2014 - 20:35:48 CST)
Topology and parameter files for some engineered residues KK R (Wed Nov 19 2014 - 09:31:33 CST)
Re: About NAMD Douglas Houston (Tue Nov 18 2014 - 09:32:59 CST)
- AW: About NAMD Norman Geist (Wed Nov 19 2014 - 01:10:11 CST)
  - Re: AW: About NAMD Douglas Houston (Wed Nov 26 2014 - 05:28:39 CST)
NAMD 2.10b2 released Jim Phillips (Mon Nov 17 2014 - 14:22:52 CST)
Colvar: minimal distance between 2 groups of atoms Vlad Cojocaru (Mon Nov 17 2014 - 07:41:31 CST)
- Re: Colvar: minimal distance between 2 groups of atoms Giacomo Fiorin (Mon Nov 17 2014 - 08:49:18 CST)
  - Re: Colvar: minimal distance between 2 groups of atoms Vlad Cojocaru (Mon Nov 17 2014 - 09:57:37 CST)
how to fix the problem Liqun Zhang (Fri Nov 14 2014 - 17:19:37 CST)
- Re: how to fix the problem Jeff Comer (Fri Nov 14 2014 - 20:02:09 CST)
  - Re: how to fix the problem Jeff Comer (Fri Nov 14 2014 - 20:02:44 CST)
  - Re: how to fix the problem Jeff Comer (Sat Nov 15 2014 - 08:33:54 CST)
water-protein interation sunyeping (Fri Nov 14 2014 - 02:32:11 CST)
- RE: water-protein interation Hongbo Du (Fri Nov 14 2014 - 09:03:37 CST)
Atomselect for coor, vel, xsc Kevin C Chan (Thu Nov 13 2014 - 22:49:02 CST)
- Re: Atomselect for coor, vel, xsc Josh Vermaas (Fri Nov 14 2014 - 08:58:29 CST)
  - Re: Atomselect for coor, vel, xsc Axel Kohlmeyer (Fri Nov 14 2014 - 09:02:47 CST)
    - Re: Atomselect for coor, vel, xsc Kevin C Chan (Fri Nov 21 2014 - 04:20:16 CST)
Umbrella Sampling in NAMD Kevin C Chan (Thu Nov 13 2014 - 10:25:13 CST)
Simulation of a membrane protein with large extracellular domains Fotis Baltoumas (Thu Nov 13 2014 - 07:30:54 CST)
- Re: Simulation of a membrane protein with large extracellular domains Josh Vermaas (Thu Nov 13 2014 - 08:35:43 CST)
- Re: Simulation of a membrane protein with large extracellular domains Jim Phillips (Thu Nov 13 2014 - 16:05:08 CST)
APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) Bin He (Thu Nov 13 2014 - 01:53:42 CST)
- Re: APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) Jim Phillips (Thu Nov 13 2014 - 15:47:52 CST)
namd simulation for solids withoy solvation Subbusinger N (Thu Nov 13 2014 - 00:02:42 CST)
- Re: namd simulation for solids withoy solvation Kenno Vanommeslaeghe (Thu Nov 13 2014 - 11:50:51 CST)
  - Re: namd simulation for solids withoy solvation Subbusinger N (Fri Nov 14 2014 - 00:20:24 CST)
unsubscribe Gurpreet Kaur Dhindsa (Wed Nov 12 2014 - 19:04:28 CST)
Can NAMD does Langevin Dynamics Simulation Fidan Sumbul (Wed Nov 12 2014 - 14:48:25 CST)
- Re: Can NAMD does Langevin Dynamics Simulation Jeff Comer (Wed Nov 12 2014 - 16:37:31 CST)
  - Re: Can NAMD does Langevin Dynamics Simulation Fidan Sumbul (Thu Nov 13 2014 - 10:41:39 CST)
    - Re: Can NAMD does Langevin Dynamics Simulation Jeff Comer (Thu Nov 13 2014 - 14:37:13 CST)
    - Re: Can NAMD does Langevin Dynamics Simulation Jeff Comer (Thu Nov 13 2014 - 15:11:10 CST)
SOD topology with CHARMM36 Francesco Pietra (Tue Nov 11 2014 - 11:02:22 CST)
- Re: SOD topology with CHARMM36 Josh Vermaas (Tue Nov 11 2014 - 11:08:26 CST)
  - Re: SOD topology with CHARMM36 Kenno Vanommeslaeghe (Tue Nov 11 2014 - 12:27:08 CST)
Dioxygen atom type with CHARMM36 Francesco Pietra (Tue Nov 11 2014 - 10:11:00 CST)
- Re: Dioxygen atom type with CHARMM36 Kenno Vanommeslaeghe (Tue Nov 11 2014 - 11:07:25 CST)
  - Re: Dioxygen atom type with CHARMM36 Francesco Pietra (Tue Nov 11 2014 - 11:19:17 CST)
Re: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD Bin He (Mon Nov 10 2014 - 13:51:15 CST)
- AW: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD Norman Geist (Tue Nov 11 2014 - 02:48:52 CST)
- Re: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD Bin He (Tue Nov 11 2014 - 06:19:06 CST)
  - AW: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD Norman Geist (Tue Nov 11 2014 - 07:03:53 CST)
AW: FATAL ERROR: error parsing config file while executing <feff> Norman Geist (Mon Nov 10 2014 - 08:20:48 CST)
- Re: AW: FATAL ERROR: error parsing config file while executing <feff> Jim Phillips (Mon Nov 10 2014 - 15:44:39 CST)
Reg: QM/MM calculations in NAMD Akshay Bhatnagar (Mon Nov 10 2014 - 07:05:40 CST)
- AW: Reg: QM/MM calculations in NAMD Norman Geist (Mon Nov 10 2014 - 08:12:44 CST)
FATAL ERROR: error parsing config file while executing <feff> Mihaela Drenscko (Sun Nov 09 2014 - 11:39:11 CST)
- AW: FATAL ERROR: error parsing config file while executing <feff> Norman Geist (Mon Nov 10 2014 - 00:56:24 CST)
  - Re: AW: FATAL ERROR: error parsing config file while executing <feff> Jim Phillips (Mon Nov 10 2014 - 16:00:19 CST)
Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD Bin He (Sat Nov 08 2014 - 01:24:32 CST)
- AW: Why CPU Usage is low when I run ibverbs-smp-cuda version NAMD Norman Geist (Mon Nov 10 2014 - 00:53:15 CST)
multiple harmonic constrains Azadeh Alavi (Sat Nov 08 2014 - 01:36:16 CST)
- Re: multiple harmonic constrains Jeff Comer (Sat Nov 08 2014 - 14:54:50 CST)
ffTK problem: OPT.Charges Zeinab Emami (Fri Nov 07 2014 - 09:14:15 CST)
- Re: vmd-l: ffTK problem: OPT.Charges Mayne, Christopher G (Fri Nov 07 2014 - 10:51:57 CST)
  - Re: Re: vmd-l: ffTK problem: OPT.Charges Zeinab Emami (Fri Nov 07 2014 - 11:13:04 CST)
CUDA Fatal Error While Trying to Run Under Windows 8.1 Justin Sanders (Thu Nov 06 2014 - 12:01:58 CST)
- Re: CUDA Fatal Error While Trying to Run Under Windows 8.1 Branko (Thu Nov 06 2014 - 12:15:59 CST)
- Re: CUDA Fatal Error While Trying to Run Under Windows 8.1 Jim Phillips (Thu Nov 06 2014 - 13:00:35 CST)
NAMD on SLURM Abhishek TYAGI (Wed Nov 05 2014 - 23:30:20 CST)
- Re: NAMD on SLURM Mitchell Gleed (Wed Nov 12 2014 - 12:57:16 CST)
  - Re: NAMD on SLURM Abhishek TYAGI (Wed Nov 12 2014 - 21:07:16 CST)
Multiple input and output files Debashis Kundu (Wed Nov 05 2014 - 20:20:37 CST)
- å´”å¹¼æ¬ è‡ªåŠ¨å›žå¤: Multiple input and output files cuiyoutian_at_163.com (Wed Nov 05 2014 - 20:20:37 CST)
- Re: Multiple input and output files Axel Kohlmeyer (Wed Nov 05 2014 - 21:51:44 CST)
- Re: Multiple input and output files Josh Vermaas (Wed Nov 05 2014 - 20:54:02 CST)
  - Re: Multiple input and output files Jim Phillips (Thu Nov 06 2014 - 12:50:36 CST)
1-5 Intramolecular repulsions Rebecca Lindsey (Wed Nov 05 2014 - 11:54:40 CST)
- Re: 1-5 Intramolecular repulsions Kenno Vanommeslaeghe (Wed Nov 05 2014 - 12:33:12 CST)
  - Re: 1-5 Intramolecular repulsions Jeffrey Potoff (Wed Nov 05 2014 - 12:51:02 CST)
  - Re: 1-5 Intramolecular repulsions rocwhite168 (Wed Nov 05 2014 - 13:02:55 CST)
colvars fatal error Leili Zhang (Tue Nov 04 2014 - 22:44:05 CST)
- Re: colvars fatal error JÃ©rÃ´me HÃ©nin (Wed Nov 05 2014 - 02:54:43 CST)
- NAMD error LInux 3.11.10-21-desktop kernel AMD opternon 6272 Thomas C. Bishop (Wed Nov 05 2014 - 09:48:15 CST)
  - AW: NAMD error LInux 3.11.10-21-desktop kernel AMD opternon 6272 Norman Geist (Thu Nov 06 2014 - 01:43:36 CST)
  - Re: NAMD error LInux 3.11.10-21-desktop kernel AMD opternon 6272 Thomas C. Bishop (Tue Nov 11 2014 - 12:41:11 CST)
vdW-only fep between two ions Christopher Rowley (Tue Nov 04 2014 - 14:43:08 CST)
harmonic restraints between multiple atom pairs Neelanjana Sengupta (Mon Nov 03 2014 - 22:42:33 CST)
- RE: harmonic restraints between multiple atom pairs Tristan Croll (Mon Nov 03 2014 - 23:20:09 CST)
explicit membrane in implicit solvent Gisella Alfonsino (Mon Nov 03 2014 - 05:00:36 CST)
- Re: explicit membrane in implicit solvent Kenno Vanommeslaeghe (Mon Nov 03 2014 - 10:46:24 CST)
Why RDF increases as r increase instead of constant Nifeng Guo hui (Sat Nov 01 2014 - 17:07:32 CDT)
- Re: Why RDF increases as r increase instead of constant Kenno Vanommeslaeghe (Sun Nov 02 2014 - 12:38:04 CST)
  - Re: Why RDF increases as r increase instead of constant Kenno Vanommeslaeghe (Sun Nov 02 2014 - 18:25:41 CST)
- Re: Why RDF increases as r increase instead of constant Arash Azari (Mon Nov 03 2014 - 01:32:27 CST)
Reg: dielectric constant calculations in NAMD Akshay Bhatnagar (Fri Oct 31 2014 - 00:51:24 CDT)
Mechanical Properties of protein chin chun (Thu Oct 30 2014 - 19:18:11 CDT)
- Re: Mechanical Properties of protein Maxim Belkin (Thu Oct 30 2014 - 20:27:58 CDT)
SMD constant velocity not constant Charles Whidborne (Wed Oct 29 2014 - 19:25:08 CDT)
- Re: SMD constant velocity not constant Axel Kohlmeyer (Wed Oct 29 2014 - 20:04:28 CDT)
Dioxygen params charmm36 Francesco Pietra (Wed Oct 29 2014 - 16:27:17 CDT)
namd ibverbs compile target Bennion, Brian (Tue Oct 28 2014 - 18:04:52 CDT)
Carma v.1.4 released. Nicholas M Glykos (Mon Oct 27 2014 - 06:09:24 CDT)
jeremy adler jeremy adler (Thu Oct 23 2014 - 06:21:43 CDT)
Reg: error in log file Akshay Bhatnagar (Tue Oct 21 2014 - 20:36:48 CDT)
- Re: Reg: error in log file Jim Phillips (Thu Oct 30 2014 - 10:46:01 CDT)
Improving MDFF results Kevin C Chan (Mon Oct 20 2014 - 22:15:59 CDT)
- RE: Improving MDFF results Tristan Croll (Tue Oct 21 2014 - 00:36:21 CDT)
  - Re: Improving MDFF results Kevin Chun Chan (Tue Oct 21 2014 - 10:56:00 CDT)
    - Re: Improving MDFF results Tristan Croll (Tue Oct 21 2014 - 14:22:31 CDT)
running a calculation during simulation btreece_at_andrew.cmu.edu (Mon Oct 20 2014 - 16:08:12 CDT)
- Re: running a calculation during simulation Josh Vermaas (Mon Oct 20 2014 - 16:38:57 CDT)
- Re: running a calculation during simulation Maxim Belkin (Mon Oct 20 2014 - 18:00:03 CDT)
- Re: running a calculation during simulation Ajasja LjubetiÄ (Tue Oct 21 2014 - 02:52:21 CDT)
  - Re: running a calculation during simulation JÃ©rÃ´me HÃ©nin (Tue Oct 21 2014 - 04:03:13 CDT)
Graphene simualtion Abhishek TYAGI (Mon Oct 20 2014 - 03:28:51 CDT)
AW: wrapping in two dimensions Norman Geist (Mon Oct 20 2014 - 01:14:02 CDT)
Replica Exchange Simulation in NAMD Precompiled binary in single node. Nizar Masbukhin (Thu Oct 16 2014 - 17:09:05 CDT)
wrapping in two dimensions Maria Bykhovskaia (Thu Oct 16 2014 - 15:33:34 CDT)
- AW: wrapping in two dimensions Norman Geist (Fri Oct 17 2014 - 02:21:07 CDT)
AW: velocity manipulation Norman Geist (Thu Oct 16 2014 - 08:26:37 CDT)
AW: velocity manipulation Norman Geist (Thu Oct 16 2014 - 08:11:59 CDT)
velocity manipulation mostafa raeesi (Thu Oct 16 2014 - 06:37:02 CDT)
- AW: velocity manipulation Norman Geist (Thu Oct 16 2014 - 07:27:28 CDT)
- Re: velocity manipulation Axel Kohlmeyer (Thu Oct 16 2014 - 08:21:17 CDT)
  - Re: velocity manipulation Ajasja LjubetiÄ (Thu Oct 16 2014 - 08:24:34 CDT)
ffTK problem: initial parameter file is void of of atoms! Zeinab Emami (Thu Oct 16 2014 - 04:15:55 CDT)
ffTK problem: initial parameter fiel is viod of atoms! Zeinab Emami (Wed Oct 15 2014 - 07:42:57 CDT)
- Re: ffTK problem: initial parameter fiel is viod of atoms! Mayne, Christopher G (Mon Oct 20 2014 - 09:55:55 CDT)
  - Re: Re: ffTK problem: initial parameter fiel is viod of atoms! Zeinab Emami (Mon Oct 20 2014 - 11:33:25 CDT)
    - Re: Re: ffTK problem: initial parameter fiel is viod of atoms! Mayne, Christopher G (Mon Oct 20 2014 - 11:45:39 CDT)
VRPN cannot connect to Falcon George Patargias (Wed Oct 15 2014 - 04:58:11 CDT)
NAMD and usable FFs Francesco Pietra (Wed Oct 15 2014 - 04:34:31 CDT)
- Re: NAMD and usable FFs Josh Vermaas (Wed Oct 15 2014 - 09:20:08 CDT)
  - Re: NAMD and usable FFs Francesco Pietra (Thu Oct 16 2014 - 12:59:10 CDT)
- Re: NAMD and usable FFs Kenno Vanommeslaeghe (Thu Oct 16 2014 - 13:37:11 CDT)
colvars replica exchange oddity JC Gumbart (Tue Oct 14 2014 - 22:27:07 CDT)
VRPN compilation error George Patargias (Tue Oct 14 2014 - 08:43:59 CDT)
- Re: VRPN compilation error Axel Kohlmeyer (Tue Oct 14 2014 - 08:54:12 CDT)
Performance difference of prcompiled binary VS source code Nizar Masbukhin (Mon Oct 13 2014 - 19:23:43 CDT)
MPICH 3 with Namd2/Charm Daniel Strahs (Mon Oct 13 2014 - 18:04:45 CDT)
long running sim dies Thomas C. Bishop (Mon Oct 13 2014 - 08:29:43 CDT)
- Re: long running sim dies Tristan Croll (Mon Oct 13 2014 - 14:36:37 CDT)
- Re: long running sim dies ransun (Mon Oct 13 2014 - 09:12:33 CDT)
Re: vmd-l: making psf files Zeinab Emami (Mon Oct 13 2014 - 04:55:06 CDT)
- Re: Re: vmd-l: making psf files Kenno Vanommeslaeghe (Mon Oct 13 2014 - 12:18:31 CDT)
Reï¼štutorial-l: Protein structure distorted after Energy minimization with NAMD sunyeping (Wed Oct 08 2014 - 21:58:02 CDT)
Umbrella sampling tilt with respect to Z-axis Mitchell Gleed (Wed Oct 08 2014 - 15:38:29 CDT)
- Re: Umbrella sampling tilt with respect to Z-axis Giacomo Fiorin (Wed Oct 08 2014 - 15:45:04 CDT)
  - Re: Umbrella sampling tilt with respect to Z-axis Mitchell Gleed (Wed Oct 08 2014 - 18:07:00 CDT)
    - Re: Umbrella sampling tilt with respect to Z-axis Aron Broom (Wed Oct 08 2014 - 18:54:44 CDT)
question about '+devices' ukulililixl (Wed Oct 08 2014 - 01:06:50 CDT)
- AW: question about '+devices' Norman Geist (Wed Oct 08 2014 - 02:13:08 CDT)
Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Tue Oct 07 2014 - 11:30:07 CDT)
String method in NAMD 2.10b1? Jenny lou (Mon Oct 06 2014 - 12:58:17 CDT)
Parameter colvars Z (Mon Oct 06 2014 - 05:26:21 CDT)
- Re: Parameter colvars Giacomo Fiorin (Mon Oct 06 2014 - 05:45:41 CDT)
  - Re: Parameter colvars Z (Mon Oct 06 2014 - 05:56:07 CDT)
- Re: Parameter colvars Z (Mon Oct 06 2014 - 06:55:44 CDT)
Does NAMD have some way to test the result? ukulililixl (Fri Oct 03 2014 - 21:50:52 CDT)
- Re: Does NAMD have some way to test the result? Axel Kohlmeyer (Fri Oct 03 2014 - 22:17:05 CDT)
  - Re: Does NAMD have some way to test the result? JÃ©rÃ´me HÃ©nin (Sat Oct 04 2014 - 04:20:57 CDT)
Newbie GPU user, please help with my submission line Jose Borreguero (Thu Oct 02 2014 - 14:03:24 CDT)
Re: Self-Assemble Monolayer--Periodic Boundary Conditions Natnael Doilicho (Wed Oct 01 2014 - 16:14:52 CDT)
How to Amend a PBD file for NAMD Zeinab Emami (Wed Oct 01 2014 - 09:27:15 CDT)
AW: vmd-l: Stray PME grid Norman Geist (Wed Oct 01 2014 - 02:27:31 CDT)
FATAL ERROR: Setting parameter colvars from script failed! Mihaela Drenscko (Tue Sep 30 2014 - 09:27:18 CDT)
- Re: FATAL ERROR: Setting parameter colvars from script failed! JÃ©rÃ´me HÃ©nin (Tue Sep 30 2014 - 10:17:02 CDT)
  - Re: FATAL ERROR: Setting parameter colvars from script failed! JÃ©rÃ´me HÃ©nin (Tue Sep 30 2014 - 13:04:27 CDT)
  - Re: FATAL ERROR: Setting parameter colvars from script failed! JÃ©rÃ´me HÃ©nin (Tue Sep 30 2014 - 13:28:48 CDT)
Folic acid parameters Haleh a (Tue Sep 30 2014 - 08:44:38 CDT)
- Re: Folic acid parameters Fotis Baltoumas (Tue Sep 30 2014 - 10:06:43 CDT)
  - Re: Folic acid parameters Kenno Vanommeslaeghe (Tue Sep 30 2014 - 11:37:03 CDT)
    - Re: Folic acid parameters Haleh a (Wed Oct 01 2014 - 01:42:20 CDT)
- Re: Folic acid parameters Kenno Vanommeslaeghe (Tue Sep 30 2014 - 10:43:21 CDT)
Self-Assemble Monolayer--Periodic Boundary Conditions Natnael Doilicho (Mon Sep 29 2014 - 18:03:18 CDT)
- AW: Self-Assemble Monolayer--Periodic Boundary Conditions Norman Geist (Tue Sep 30 2014 - 01:38:57 CDT)
PCL dcd files Mihaela Drenscko (Mon Sep 29 2014 - 11:09:40 CDT)
- Fwd: PCL dcd files Mihaela Drenscko (Mon Sep 29 2014 - 11:38:30 CDT)
  - Re: PCL dcd files Giacomo Fiorin (Mon Sep 29 2014 - 12:10:07 CDT)
    - Re: PCL dcd files Niklaus Johner (Tue Sep 30 2014 - 01:15:25 CDT)
Molecular Dynamics of Rigid Linear Molecules in NAMD. Javad Noroozi (Sun Sep 28 2014 - 00:44:28 CDT)
- Re: Molecular Dynamics of Rigid Linear Molecules in NAMD. Mike Makowski (Sun Sep 28 2014 - 03:03:10 CDT)
  - Re: Molecular Dynamics of Rigid Linear Molecules in NAMD. Mike Makowski (Sun Sep 28 2014 - 06:50:36 CDT)
SMD pulling speed Charles Whidborne (Sat Sep 27 2014 - 20:45:48 CDT)
- Re: SMD pulling speed Giacomo Fiorin (Sat Sep 27 2014 - 21:16:15 CDT)
namd coulomb conversion factor Mohan maruthi sena (Sat Sep 27 2014 - 01:09:43 CDT)
Reg: minimization Akshay Bhatnagar (Wed Sep 24 2014 - 23:35:16 CDT)
- Re: Reg: minimization Axel Kohlmeyer (Wed Sep 24 2014 - 23:44:35 CDT)
  - Re: Reg: minimization Akshay Bhatnagar (Thu Sep 25 2014 - 04:51:52 CDT)
  - Re: Reg: minimization Akshay Bhatnagar (Thu Sep 25 2014 - 04:52:40 CDT)
    - AW: Reg: minimization Norman Geist (Thu Sep 25 2014 - 05:23:26 CDT)
getting different dihedral energy with two identical backbones Joyce Yang (Wed Sep 24 2014 - 16:45:52 CDT)
- Re: getting different dihedral energy with two identical backbones Jim Phillips (Fri Sep 26 2014 - 17:18:24 CDT)
  - Re: getting different dihedral energy with two identical backbones Joyce Yang (Mon Sep 29 2014 - 21:15:54 CDT)
expected speed up after fixing atoms? Jose Borreguero (Wed Sep 24 2014 - 12:44:48 CDT)
- Re: expected speed up after fixing atoms? Aron Broom (Wed Sep 24 2014 - 13:10:45 CDT)
  - Re: expected speed up after fixing atoms? Jose Borreguero (Wed Sep 24 2014 - 13:41:02 CDT)
- Re: expected speed up after fixing atoms? Kenno Vanommeslaeghe (Wed Sep 24 2014 - 14:06:46 CDT)
Problem with running namdenergy plugin from text interface zeynab mohamad hoseyni (Mon Sep 22 2014 - 14:53:04 CDT)
- Re: Problem with running namdenergy plugin from text interface Josh Vermaas (Mon Sep 22 2014 - 15:09:10 CDT)
  - Re: Problem with running namdenergy plugin from text interface zeynab mohamad hoseyni (Mon Sep 22 2014 - 22:29:26 CDT)
which namd versions compatible with CUDA 5.5 and other CUDA woes Robert Wohlhueter (Mon Sep 22 2014 - 13:39:19 CDT)
- Re: which namd versions compatible with CUDA 5.5 and other CUDA woes Jim Phillips (Fri Sep 26 2014 - 17:25:29 CDT)
  - Re: which namd versions compatible with CUDA 5.5 and other CUDA woes Robert Wohlhueter (Sun Sep 28 2014 - 12:00:17 CDT)
Re: Is there any point in running NAMD over an ethernet-linked cluster? Nicholas M Glykos (Sun Sep 21 2014 - 13:21:53 CDT)
- Re: Is there any point in running NAMD over an ethernet-linked cluster? Douglas Houston (Mon Sep 22 2014 - 00:23:41 CDT)
  - Re: Is there any point in running NAMD over an ethernet-linked cluster? Axel Kohlmeyer (Mon Sep 22 2014 - 01:22:11 CDT)
Simulation Do not Run in the Cluster Roy Fernando (Sun Sep 21 2014 - 12:16:44 CDT)
Implicit solvent lipid bilayer simulation in NAMD. Subbarao Kanchi (Wed Sep 17 2014 - 12:04:44 CDT)
- Re: Implicit solvent lipid bilayer simulation in NAMD. Siva Dasetty (Wed Sep 17 2014 - 13:23:53 CDT)
  - Re: Implicit solvent lipid bilayer simulation in NAMD. Subbarao Kanchi (Wed Sep 17 2014 - 13:41:34 CDT)
simulation options available with GPU Ana Celia Vila Verde (Tue Sep 16 2014 - 02:52:51 CDT)
Constraining two sets of atoms Natnael Doilicho (Tue Sep 16 2014 - 12:06:38 CDT)
simulation options available with GPU Ana Celia Vila Verde (Tue Sep 16 2014 - 02:58:28 CDT)
Setting constraints for SMD simulation Charles Whidborne (Mon Sep 15 2014 - 20:20:39 CDT)
Annealing process of silica with excluded block Marzieh Alishahi (Fri Sep 12 2014 - 10:22:51 CDT)
- Re: Annealing process of silica with excluded block Jeff Comer (Mon Sep 15 2014 - 09:30:57 CDT)
  - Re: Annealing process of silica with excluded block Marzieh Alishahi (Mon Sep 15 2014 - 09:40:21 CDT)
Qh Lurong Pan (Thu Sep 11 2014 - 08:22:22 CDT)
Unsubscribe Katherine Parra (Wed Sep 10 2014 - 09:12:24 CDT)
I would like to unsubscribe Maria Kopp (Wed Sep 10 2014 - 09:04:54 CDT)
- Re: I would like to unsubscribe MEHRAN MB (Wed Sep 10 2014 - 09:19:54 CDT)
- Re: I would like to unsubscribe Giacomo Fiorin (Wed Sep 10 2014 - 09:21:11 CDT)
- Re: I would like to unsubscribe Ajasja LjubetiÄ (Wed Sep 10 2014 - 10:03:21 CDT)
Colvars simulation running slow? Tristan Croll (Tue Sep 09 2014 - 20:31:06 CDT)
- Re: Colvars simulation running slow? JÃ©rÃ´me HÃ©nin (Wed Sep 10 2014 - 02:13:00 CDT)
  - RE: Colvars simulation running slow? Tristan Croll (Wed Sep 10 2014 - 17:15:35 CDT)
    - RE: Colvars simulation running slow? Tristan Croll (Wed Sep 10 2014 - 19:51:15 CDT)
    - Re: Colvars simulation running slow? Ajasja LjubetiÄ (Wed Sep 10 2014 - 19:58:48 CDT)
GBIS using CUDA enabled NAMD Siva Dasetty (Tue Sep 09 2014 - 18:59:01 CDT)
- Re: GBIS using CUDA enabled NAMD David Hardy (Wed Sep 10 2014 - 14:46:22 CDT)
- Re: GBIS using CUDA enabled NAMD Jim Phillips (Wed Sep 10 2014 - 16:32:32 CDT)
  - Re: GBIS using CUDA enabled NAMD Siva Dasetty (Wed Sep 17 2014 - 09:36:03 CDT)
[ANN] MDTraj 1.0: Trajectory Analysis in Python Robert McGibbon (Mon Sep 08 2014 - 17:19:00 CDT)
- Re: [ANN] MDTraj 1.0: Trajectory Analysis in Python Ivan Gregoretti (Tue Sep 09 2014 - 12:09:49 CDT)
Unable to read corrupted binary DCD trajectory file Viswanath Pasumarthi (Mon Sep 08 2014 - 09:04:32 CDT)
- Re: Unable to read corrupted binary DCD trajectory file Branko (Mon Sep 08 2014 - 09:13:35 CDT)
  - Re: Unable to read corrupted binary DCD trajectory file Viswanath Pasumarthi (Mon Sep 08 2014 - 09:38:31 CDT)
  - Re: Unable to read corrupted binary DCD trajectory file Viswanath Pasumarthi (Mon Sep 08 2014 - 15:27:12 CDT)
    - Re: Unable to read corrupted binary DCD trajectory file Kenno Vanommeslaeghe (Mon Sep 08 2014 - 16:38:48 CDT)
- Re: Unable to read corrupted binary DCD trajectory file Andreas Förster (Mon Sep 08 2014 - 09:29:51 CDT)
  - Re: Unable to read corrupted binary DCD trajectory file Viswanath Pasumarthi (Mon Sep 08 2014 - 09:43:47 CDT)
- Re: Unable to read corrupted binary DCD trajectory file Gergely Gyimesi (Mon Sep 08 2014 - 09:51:33 CDT)
GBIS CUDA not yet compatible with fixed atoms Siva Dasetty (Fri Sep 05 2014 - 10:03:12 CDT)
- Re: GBIS CUDA not yet compatible with fixed atoms Jim Phillips (Fri Sep 05 2014 - 15:16:04 CDT)
  - Re: GBIS CUDA not yet compatible with fixed atoms Siva Dasetty (Fri Sep 05 2014 - 15:24:45 CDT)
    - Re: GBIS CUDA not yet compatible with fixed atoms Aron Broom (Fri Sep 05 2014 - 16:50:39 CDT)
    - Re: GBIS CUDA not yet compatible with fixed atoms Siva Dasetty (Fri Sep 05 2014 - 18:01:13 CDT)
SASA calculation Siva Dasetty (Thu Sep 04 2014 - 09:03:56 CDT)
FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small. Sandhyaa Subramanian (Wed Sep 03 2014 - 02:34:06 CDT)
Question to NAMD source Norman Geist (Thu Sep 04 2014 - 08:02:31 CDT)
- Re: Question to NAMD source Jim Phillips (Thu Sep 04 2014 - 11:25:48 CDT)
  - AW: Question to NAMD source Norman Geist (Fri Sep 05 2014 - 01:32:29 CDT)
Alignment Zeinab Emami (Thu Sep 04 2014 - 07:12:14 CDT)
- Re: Alignment Axel Kohlmeyer (Thu Sep 04 2014 - 07:53:23 CDT)
efficient way to apply time-dependent electric field Azadeh Alavi (Thu Sep 04 2014 - 05:38:12 CDT)
- Re: efficient way to apply time-dependent electric field Jim Phillips (Thu Sep 04 2014 - 11:18:00 CDT)
computing forces on atoms by postprocessing a dcd file generated with FEP enabled Harris, Robert C. (Wed Sep 03 2014 - 14:05:40 CDT)
INCONSISTENCY messages and minimization in toturial 1-2-sphere Yan Zhou (Wed Sep 03 2014 - 03:14:30 CDT)
FEP, Ewald size-dependence charge correction Sebastian Stolzenberg (Tue Sep 02 2014 - 15:12:17 CDT)
- Re: FEP, Ewald size-dependence charge correction Sebastian Stolzenberg (Sun Sep 07 2014 - 10:23:17 CDT)
  - Re: FEP, Ewald size-dependence charge correction Sebastian Stolzenberg (Fri Sep 12 2014 - 13:21:10 CDT)
    - Re: FEP, Ewald size-dependence charge correction JC Gumbart (Sat Sep 13 2014 - 18:38:44 CDT)
FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small. Sandhyaa Subramanian (Sat Aug 30 2014 - 09:06:14 CDT)
- RE: FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small. Tristan Croll (Tue Sep 02 2014 - 17:27:20 CDT)
  - RE: FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small. Tristan Croll (Wed Sep 03 2014 - 02:26:27 CDT)
    - Re: FATAL ERROR: Low global exclusion count! (9231 vs 9270) System unstable or pairlistdist or cutoff too small. Sandhyaa Subramanian (Wed Sep 03 2014 - 02:37:32 CDT)
problems running ABF simulation Charles Whidborne (Tue Sep 02 2014 - 00:37:40 CDT)
- Re: problems running ABF simulation Giacomo Fiorin (Tue Sep 02 2014 - 02:45:26 CDT)
Re: Fixing atoms while equilibration Siva Dasetty (Mon Sep 01 2014 - 07:33:57 CDT)
- Re: Fixing atoms while equilibration Axel Kohlmeyer (Mon Sep 01 2014 - 07:48:34 CDT)
  - Re: Fixing atoms while equilibration Siva Dasetty (Mon Sep 01 2014 - 08:07:59 CDT)
    - Re: Fixing atoms while equilibration Axel Kohlmeyer (Mon Sep 01 2014 - 08:14:37 CDT)
    - Re: Fixing atoms while equilibration Kenno Vanommeslaeghe (Mon Sep 01 2014 - 10:52:07 CDT)
problem in calculating binding energy using MMGBSA with namd-2.9 Shailesh Pandey (Mon Sep 01 2014 - 07:31:34 CDT)
Reg: solvation in DMSO Akshay Bhatnagar (Mon Sep 01 2014 - 00:01:44 CDT)
- Fwd: Reg: solvation in DMSO Akshay Bhatnagar (Wed Sep 03 2014 - 02:36:04 CDT)
  - Re: Fwd: Reg: solvation in DMSO Kenno Vanommeslaeghe (Wed Sep 03 2014 - 14:43:59 CDT)
restraining bonds Neelanjana Sengupta (Sun Aug 31 2014 - 23:50:24 CDT)
- RE: restraining bonds Tristan Croll (Mon Sep 01 2014 - 00:45:22 CDT)
  - RE: restraining bonds Tristan Croll (Mon Sep 01 2014 - 00:57:28 CDT)
  - RE: restraining bonds Tristan Croll (Mon Sep 01 2014 - 01:09:05 CDT)
    - Re: restraining bonds Kenno Vanommeslaeghe (Mon Sep 01 2014 - 10:37:17 CDT)
    - Re: restraining bonds Kenno Vanommeslaeghe (Tue Sep 02 2014 - 11:04:37 CDT)
NAMD energy minimization Siva Dasetty (Sun Aug 31 2014 - 14:30:56 CDT)
- Re: NAMD energy minimization Axel Kohlmeyer (Sun Aug 31 2014 - 14:51:10 CDT)
RDF calculation of crystal system Fatemeh Omidbeygi (Sat Aug 30 2014 - 00:41:02 CDT)
- Re: RDF calculation of crystal system Axel Kohlmeyer (Sat Aug 30 2014 - 01:49:16 CDT)
Fixing atoms while equilibration Siva Dasetty (Fri Aug 29 2014 - 20:12:21 CDT)
- AW: Fixing atoms while equilibration Norman Geist (Mon Sep 01 2014 - 02:26:11 CDT)
Re: ibverb&&smp build NAMD ukulililixl (Fri Aug 29 2014 - 06:41:21 CDT)
- AW: ibverb&&smp build NAMD Norman Geist (Mon Sep 01 2014 - 02:17:13 CDT)
Assessing convergence in FEP calculations Gianluca Interlandi (Thu Aug 28 2014 - 14:00:08 CDT)
Combining interleaved and top posting is considered harmful. Nicholas M Glykos (Thu Aug 28 2014 - 11:11:40 CDT)
- Re: Combining interleaved and top posting is considered harmful. Jim Phillips (Thu Aug 28 2014 - 11:29:10 CDT)
Set exact molarity in cell Stephan Grein (Thu Aug 28 2014 - 09:08:42 CDT)
ibverb&&smp build NAMD ukulililixl (Thu Aug 28 2014 - 04:30:47 CDT)
- AW: ibverb&&smp build NAMD Norman Geist (Thu Aug 28 2014 - 05:25:13 CDT)
(no subject) BIPLAB NANDI (Wed Aug 27 2014 - 22:13:06 CDT)
- Re: Gianluca Interlandi (Thu Aug 28 2014 - 00:16:37 CDT)
Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Wed Aug 27 2014 - 13:05:05 CDT)
Window for FEP calculations Gianluca Interlandi (Tue Aug 26 2014 - 19:35:33 CDT)
NAMD 2.10b1 CUDA PME offload Norman Geist (Tue Aug 26 2014 - 09:25:48 CDT)
- Re: NAMD 2.10b1 CUDA PME offload Jim Phillips (Tue Aug 26 2014 - 10:22:48 CDT)
- AW: NAMD 2.10b1 CUDA PME offload Norman Geist (Tue Aug 26 2014 - 10:24:50 CDT)
Metadynamics test along eigenvector Floquet Nicolas (Tue Aug 26 2014 - 02:58:00 CDT)
- Re: Metadynamics test along eigenvector Giacomo Fiorin (Tue Aug 26 2014 - 10:07:34 CDT)
(no subject) ukulililixl (Tue Aug 26 2014 - 01:22:20 CDT)
- Re: Jim Phillips (Tue Aug 26 2014 - 10:38:36 CDT)
Siginificant speedup by updating nvidia driver Norman Geist (Mon Aug 25 2014 - 11:06:38 CDT)
Nucleic acid stains parameters SebastiÃ¡n GutiÃ©rrez (Mon Aug 25 2014 - 10:37:04 CDT)
- Re: Nucleic acid stains parameters Kenno Vanommeslaeghe (Mon Aug 25 2014 - 10:56:26 CDT)
Metadynamics with eigenvector Nicolas Floquet (Mon Aug 25 2014 - 09:40:06 CDT)
- Re: Metadynamics with eigenvector Giacomo Fiorin (Mon Aug 25 2014 - 10:17:22 CDT)
NAMD 2.10b1 released Jim Phillips (Mon Aug 25 2014 - 07:49:51 CDT)
question in NAMD with icc & cuda ukulililixl (Mon Aug 25 2014 - 06:40:48 CDT)
ABF hBond Charles Whidborne (Mon Aug 25 2014 - 02:52:45 CDT)
- Re: ABF hBond Giacomo Fiorin (Mon Aug 25 2014 - 10:18:12 CDT)
AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. Norman Geist (Fri Aug 22 2014 - 08:21:25 CDT)
- Re: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. Maxime Boissonneault (Fri Aug 22 2014 - 08:22:43 CDT)
  - AW: AW: AW: FATAL ERROR: PME offload requires exactly one CUDA device per process. Norman Geist (Fri Aug 22 2014 - 08:56:32 CDT)
FATAL ERROR: PME offload requires exactly one CUDA device per process. Maxime Boissonneault (Fri Aug 22 2014 - 06:40:06 CDT)
Re: NAMD 2.10 Manual Ajasja LjubetiÄ (Fri Aug 22 2014 - 03:30:05 CDT)
- AW: NAMD 2.10 Manual Norman Geist (Fri Aug 22 2014 - 08:46:07 CDT)
NAMD 2.10 Manual Norman Geist (Fri Aug 22 2014 - 03:14:47 CDT)
Installation Protocol of NAMD on Linux Cluster Viswanath Pasumarthi (Thu Aug 21 2014 - 14:46:27 CDT)
SMP vs Multicore Maxime Boissonneault (Thu Aug 21 2014 - 09:26:43 CDT)
Fwd: [External] Boost value in aMD simulation Thomas Evangelidis (Thu Aug 21 2014 - 06:05:05 CDT)
- Re: [External] Boost value in aMD simulation James Starlight (Fri Aug 22 2014 - 11:54:05 CDT)
wrapping a protein Maria Bykhovskaia (Wed Aug 20 2014 - 17:40:30 CDT)
- Re: wrapping a protein Maxim Belkin (Wed Aug 20 2014 - 17:53:46 CDT)
Accelerated molecular dynamics: Energy value in output file Kapil jain (Tue Aug 19 2014 - 23:53:20 CDT)
using CHARMM-format Amber parameters in NAMD Basheer Subei (Tue Aug 19 2014 - 19:16:43 CDT)
- Re: using CHARMM-format Amber parameters in NAMD Mike Makowski (Tue Aug 19 2014 - 23:34:13 CDT)
  - Re: using CHARMM-format Amber parameters in NAMD Kenno Vanommeslaeghe (Wed Aug 20 2014 - 10:27:20 CDT)
    - Re: using CHARMM-format Amber parameters in NAMD Basheer (Wed Aug 20 2014 - 22:15:22 CDT)
"Beefier" benchmark Maxime Boissonneault (Tue Aug 19 2014 - 10:48:30 CDT)
- Re: "Beefier" benchmark Phil Greer (Tue Aug 19 2014 - 11:10:28 CDT)
  - Re: "Beefier" benchmark Maxime Boissonneault (Tue Aug 19 2014 - 11:14:31 CDT)
  - Re: "Beefier" benchmark Aron Broom (Tue Aug 19 2014 - 11:15:29 CDT)
Fwd: [External] Boost value in aMD simulation Thomas Evangelidis (Tue Aug 19 2014 - 05:24:17 CDT)
- Re: [External] Boost value in aMD simulation James Starlight (Tue Aug 19 2014 - 13:45:58 CDT)
NVT, NPT, order & combination Zeinab Emami (Tue Aug 19 2014 - 03:23:26 CDT)
- Re: NVT, NPT, order & combination Kenno Vanommeslaeghe (Tue Aug 19 2014 - 12:17:27 CDT)
Atom selection in Tcl Force script with Amber partop file Daniel Torrente (Fri Aug 15 2014 - 12:25:49 CDT)
- Re: Atom selection in Tcl Force script with Amber partop file Maxim Belkin (Fri Aug 15 2014 - 16:48:12 CDT)
  - Re: Atom selection in Tcl Force script with Amber partop file Daniel Torrente (Fri Aug 15 2014 - 18:25:23 CDT)
  - Re: Atom selection in Tcl Force script with Amber partop file Daniel Torrente (Fri Aug 15 2014 - 18:21:23 CDT)
    - Re: Atom selection in Tcl Force script with Amber partop file Maxim Belkin (Fri Aug 15 2014 - 18:33:18 CDT)
    - Re: Atom selection in Tcl Force script with Amber partop file Daniel Torrente (Fri Aug 15 2014 - 19:01:23 CDT)
Martini forcefield RBCG and ENM Raul Araya (Fri Aug 15 2014 - 10:05:01 CDT)
Hwo to switch from NPT to NVT Zeinab Emami (Fri Aug 15 2014 - 07:14:05 CDT)
Hwo to switch from NPT to NVT Zeinab Emami (Fri Aug 15 2014 - 07:12:39 CDT)
H-Bond measurements Stephan Grein (Thu Aug 14 2014 - 01:57:40 CDT)
Hybrid MPI + Multicore + Cuda build Maxime Boissonneault (Wed Aug 13 2014 - 11:46:59 CDT)
- AW: Hybrid MPI + Multicore + Cuda build Norman Geist (Thu Aug 14 2014 - 02:13:32 CDT)
  - Re: AW: Hybrid MPI + Multicore + Cuda build Maxime Boissonneault (Thu Aug 14 2014 - 07:19:37 CDT)
Root mean square deviation.......... Gurpreet Kaur Dhindsa (Tue Aug 12 2014 - 12:58:38 CDT)
Announcement: Hands-On Workshop On Computational Biophysics Danielle Chandler (Tue Aug 12 2014 - 09:31:17 CDT)
NAMD CVS_CUDA ERROR: "all CUDA-capable devices are busy or unavailable" Samuel Bowerman (Mon Aug 11 2014 - 11:50:45 CDT)
Running NAMD via GROMACS topology Mike Makowski (Sun Aug 10 2014 - 17:44:35 CDT)
- Re: Running NAMD via GROMACS topology Mike Makowski (Sun Aug 10 2014 - 18:05:21 CDT)
  - AW: Running NAMD via GROMACS topology Norman Geist (Mon Aug 11 2014 - 00:33:15 CDT)
Unsubscribe Katherine Parra (Sun Aug 10 2014 - 11:30:22 CDT)
(no subject) Shalton Evans (Sat Aug 09 2014 - 23:00:48 CDT)
Energy term in output file of Accelerated dynamics Kapil jain (Fri Aug 08 2014 - 02:14:56 CDT)
- Re: Energy term in output file of Accelerated dynamics Kapil jain (Sun Aug 10 2014 - 21:39:32 CDT)
ABF simulation, free energy to remove a DNA strand Charles Whidborne (Tue Aug 05 2014 - 01:54:14 CDT)
- Re: ABF simulation, free energy to remove a DNA strand JÃ©rÃ´me HÃ©nin (Tue Aug 05 2014 - 03:15:46 CDT)
  - Re: ABF simulation, free energy to remove a DNA strand Thomas C. Bishop (Tue Aug 05 2014 - 10:17:07 CDT)
(no subject) sudipta.mml (Sat Aug 02 2014 - 20:01:46 CDT)
Intermolecular potential energy function in NAMD Viswanath Pasumarthi (Fri Aug 01 2014 - 06:31:21 CDT)
- Re: Intermolecular potential energy function in NAMD Kenno Vanommeslaeghe (Fri Aug 01 2014 - 11:41:46 CDT)
Silent crash NAMD-multicore-CUDA MEHRAN MB (Wed Jul 30 2014 - 17:23:10 CDT)
- Re: Silent crash NAMD-multicore-CUDA Aron Broom (Wed Jul 30 2014 - 17:50:54 CDT)
  - Re: Silent crash NAMD-multicore-CUDA MEHRAN MB (Thu Jul 31 2014 - 18:27:55 CDT)
    - Re: Silent crash NAMD-multicore-CUDA MEHRAN MB (Tue Aug 19 2014 - 11:06:34 CDT)
    - Re: Silent crash NAMD-multicore-CUDA Aron Broom (Tue Aug 19 2014 - 11:17:04 CDT)
Loss of Translational entropy calculation in FEP Daniel Torrente (Wed Jul 30 2014 - 16:57:08 CDT)
+p option on Windows 7 Kukol, Andreas (Wed Jul 30 2014 - 09:56:28 CDT)
Kb, Ktheta values for TIP3P water model Viswanath Pasumarthi (Tue Jul 29 2014 - 16:38:28 CDT)
- Re: Kb, Ktheta values for TIP3P water model Hadi (Tue Jul 29 2014 - 17:59:19 CDT)
  - Re: Kb, Ktheta values for TIP3P water model Kenno Vanommeslaeghe (Tue Jul 29 2014 - 23:21:58 CDT)
- Re: Kb, Ktheta values for TIP3P water model Maxim Belkin (Mon Aug 11 2014 - 18:05:41 CDT)
Analysis problem (Data vector empty) Stephan Grein (Tue Jul 29 2014 - 04:06:27 CDT)
temperature for lipid-protein assembly Bala subramanian (Mon Jul 28 2014 - 10:19:10 CDT)
- Re: temperature for lipid-protein assembly Kenno Vanommeslaeghe (Mon Jul 28 2014 - 10:57:41 CDT)
  - Re: temperature for lipid-protein assembly Bala subramanian (Mon Jul 28 2014 - 12:06:34 CDT)
Rule of thumb for equilibration Stephan Grein (Mon Jul 28 2014 - 09:45:43 CDT)
- Re: Rule of thumb for equilibration Aron Broom (Mon Jul 28 2014 - 09:59:04 CDT)
segmentation fault in accelMD Anna Modzelewska (Mon Jul 28 2014 - 05:56:05 CDT)
REï¼š The water box shrinks at the start of the MD simulation sunyeping (Sun Jul 27 2014 - 19:19:15 CDT)
The water box shrinks at the start of the MD simulation Zheng Fulu (Sun Jul 27 2014 - 13:53:55 CDT)
The water box shrinks at the start of the MD simulation #ZHENG FULU# (Sun Jul 27 2014 - 06:13:52 CDT)
Fwd: membrane lipid involvement of cholesterol Thomas Evangelidis (Sat Jul 26 2014 - 06:39:30 CDT)
Accelerated MD (aMD) Ramin Ekhteiari (Sat Jul 26 2014 - 06:06:25 CDT)
- Re: Accelerated MD (aMD) Thomas Evangelidis (Sat Jul 26 2014 - 06:38:20 CDT)
- Re: vmd-l: Accelerated MD (aMD) Juan R. Perilla (Sun Jul 27 2014 - 20:23:00 CDT)
membrane lipid involvement of cholesterol Ramin Ekhteiari (Sat Jul 26 2014 - 03:14:38 CDT)
- RE: vmd-l: membrane lipid involvement of cholesterol Richard Wood (Sat Jul 26 2014 - 06:26:59 CDT)
  - RE: vmd-l: membrane lipid involvement of cholesterol Richard Wood (Sat Jul 26 2014 - 09:07:57 CDT)
FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C NH3 (ATOMS 105 107) Cenk Denktas (Fri Jul 25 2014 - 15:30:40 CDT)
- Re: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C NH3 (ATOMS 105 107) Kenno Vanommeslaeghe (Fri Jul 25 2014 - 16:44:15 CDT)
Loading and analysis of DCD file (~300 MB) Stephan Grein (Thu Jul 24 2014 - 06:18:45 CDT)
- Re: Loading and analysis of DCD file (~300 MB) Stephan Grein (Thu Jul 24 2014 - 06:45:54 CDT)
- Re: Loading and analysis of DCD file (~300 MB) tillmann.utesch_at_mailbox.tu-berlin.de (Thu Jul 24 2014 - 07:00:09 CDT)
  - Re: Loading and analysis of DCD file (~300 MB) Stephan Grein (Thu Jul 24 2014 - 07:02:53 CDT)
    - Re: Loading and analysis of DCD file (~300 MB) Ajasja LjubetiÄ (Thu Jul 24 2014 - 09:30:12 CDT)
Reg: LangevinPistonDecay and LangevinPistonPeriod Akshay Bhatnagar (Thu Jul 24 2014 - 02:04:25 CDT)
Re: [External] Boost value in aMD simulation James Starlight (Wed Jul 23 2014 - 14:24:45 CDT)
- Re: [External] Boost value in aMD simulation Thomas Evangelidis (Wed Jul 23 2014 - 15:02:25 CDT)
  - Re: [External] Boost value in aMD simulation James Starlight (Wed Jul 23 2014 - 15:32:53 CDT)
    - Re: [External] Boost value in aMD simulation Thomas Evangelidis (Wed Jul 23 2014 - 16:37:47 CDT)
    - Re: [External] Boost value in aMD simulation James Starlight (Thu Jul 24 2014 - 01:13:09 CDT)
- Re: [External] Boost value in aMD simulation James Starlight (Mon Aug 18 2014 - 03:25:53 CDT)
  - Re: [External] Boost value in aMD simulation Thomas Evangelidis (Mon Aug 18 2014 - 04:21:25 CDT)
    - Re: [External] Boost value in aMD simulation James Starlight (Tue Aug 19 2014 - 04:56:58 CDT)
Boost value in aMD simulation James Starlight (Wed Jul 23 2014 - 06:30:12 CDT)
NAMD_energy_plot sananda chatterjee (Tue Jul 22 2014 - 17:08:56 CDT)
- Re: NAMD_energy_plot Jason Swails (Tue Jul 22 2014 - 17:22:29 CDT)
(no subject) Carlos Navarrro Retamal (Tue Jul 22 2014 - 11:43:10 CDT)
- Re: Kenno Vanommeslaeghe (Tue Jul 22 2014 - 11:58:25 CDT)
(no subject) Mitul Saha (Tue Jul 22 2014 - 11:27:04 CDT)
- Re: Aaron Larsen (Tue Jul 22 2014 - 11:38:27 CDT)
  - Re: JÃ©rÃ´me HÃ©nin (Tue Jul 22 2014 - 11:57:54 CDT)
ABF/colvar error in NAMD2.9 Harish Vashisth (Tue Jul 22 2014 - 11:23:13 CDT)
- Re: ABF/colvar error in NAMD2.9 JÃ©rÃ´me HÃ©nin (Tue Jul 22 2014 - 11:29:47 CDT)
  - Re: ABF/colvar error in NAMD2.9 Niklaus Johner (Tue Jul 22 2014 - 13:32:12 CDT)
    - Re: ABF/colvar error in NAMD2.9 Harish Vashisth (Tue Jul 22 2014 - 14:39:15 CDT)
- Re: ABF/colvar error in NAMD2.9 Aron Broom (Tue Jul 22 2014 - 11:30:49 CDT)
  - Re: ABF/colvar error in NAMD2.9 JÃ©rÃ´me HÃ©nin (Tue Jul 22 2014 - 11:56:06 CDT)
Subject: RE: Re:Subject: Re: Subject: Re:Re: New partial charges after patching Sadegh Faramarzi Ganjabad (Tue Jul 22 2014 - 06:28:57 CDT)
Cost of a colvar calculation George Patargias (Tue Jul 22 2014 - 06:27:52 CDT)
- Re: Cost of a colvar calculation JÃ©rÃ´me HÃ©nin (Tue Jul 22 2014 - 06:56:42 CDT)
  - Re: Cost of a colvar calculation Ivan Gregoretti (Tue Jul 22 2014 - 07:33:14 CDT)
- Re: Cost of a colvar calculation Jo, Sunhwan (Tue Jul 22 2014 - 13:06:12 CDT)
  - Re: Cost of a colvar calculation Giacomo Fiorin (Tue Jul 22 2014 - 17:31:23 CDT)
    - Re: Cost of a colvar calculation Jo, Sunhwan (Tue Jul 22 2014 - 19:02:20 CDT)
Subject: Re: Subject: Re: Subject: Re:Re: New partial charges after patching Sadegh Faramarzi Ganjabad (Tue Jul 22 2014 - 05:04:09 CDT)
- 2-residue patch for Asn-Lys side chain amide bond Kenno Vanommeslaeghe (Fri Jul 25 2014 - 12:20:46 CDT)
Inquiry about forceConstant Mo Chen (Mon Jul 21 2014 - 15:03:30 CDT)
- Re: Inquiry about forceConstant Aron Broom (Mon Jul 21 2014 - 15:12:06 CDT)
  - Re: Inquiry about forceConstant Mo Chen (Mon Jul 21 2014 - 15:23:06 CDT)
    - Re: Inquiry about forceConstant Mo Chen (Mon Jul 21 2014 - 16:57:15 CDT)
    - Re: Inquiry about forceConstant JÃ©rÃ´me HÃ©nin (Tue Jul 22 2014 - 04:37:30 CDT)
Reg: deciding cell basis vector Akshay Bhatnagar (Mon Jul 21 2014 - 08:57:57 CDT)
- Re: Reg: deciding cell basis vector Aron Broom (Mon Jul 21 2014 - 12:39:39 CDT)
exchange force constants Lu Hong (Mon Jul 21 2014 - 08:50:24 CDT)
- Re: exchange force constants Sunhwan Jo (Mon Jul 21 2014 - 09:30:08 CDT)
  - RE: exchange force constants Lu Hong (Mon Jul 21 2014 - 11:25:25 CDT)
Calculating the force needed to constrain a protein Shane.OMahony (Fri Jul 18 2014 - 11:18:05 CDT)
- Re: Calculating the force needed to constrain a protein Maxim Belkin (Fri Jul 18 2014 - 11:43:27 CDT)
School on Molecular Dynamics with NAMD and LAMMPS in Philadelphia, August 18-22 2014 Axel Kohlmeyer (Thu Jul 17 2014 - 14:48:33 CDT)
running Linux-x86_64-multicore precompiled version at 2 hexa-core CPUs? Andras Borosy (Thu Jul 17 2014 - 09:27:46 CDT)
- Re: running Linux-x86_64-multicore precompiled version at 2 hexa-core CPUs? Axel Kohlmeyer (Thu Jul 17 2014 - 09:35:59 CDT)
NAMD/MIC & CUDA on Stampede Jeffery Klauda (Wed Jul 16 2014 - 13:28:27 CDT)
- Re: NAMD/MIC & CUDA on Stampede Maxim Belkin (Wed Jul 16 2014 - 15:44:34 CDT)
- Re: NAMD/MIC & CUDA on Stampede Maxim Belkin (Thu Jul 17 2014 - 13:32:27 CDT)
Re:Subject: Re: Subject: Re:Re: New partial charges after patching Sadegh Faramarzi Ganjabad (Wed Jul 16 2014 - 01:27:52 CDT)
- Re: Subject: Re: Subject: Re:Re: New partial charges after patching Kenno Vanommeslaeghe (Wed Jul 16 2014 - 12:53:47 CDT)
- RE: Re:Subject: Re: Subject: Re:Re: New partial charges after patching Tristan Croll (Wed Jul 16 2014 - 18:44:39 CDT)
RE: Force field design Gianluca Interlandi (Wed Jul 16 2014 - 00:32:49 CDT)
- Re: Force field design Sunhwan Jo (Wed Jul 16 2014 - 07:37:19 CDT)
autopsf (patch) Cenk Denktas (Tue Jul 15 2014 - 12:41:48 CDT)
Force field design Abhishek TYAGI (Tue Jul 15 2014 - 11:55:35 CDT)
- Re: Force field design Aron Broom (Tue Jul 15 2014 - 21:58:07 CDT)
  - Re: Force field design Kenno Vanommeslaeghe (Wed Jul 16 2014 - 12:06:23 CDT)
  - Re: Force field design Kenno Vanommeslaeghe (Tue Jul 22 2014 - 10:40:37 CDT)
- Re: Force field design Gianluca Interlandi (Tue Jul 15 2014 - 22:32:35 CDT)
- Re: Force field design Mayne, Christopher G (Wed Jul 16 2014 - 10:46:48 CDT)
- Re: Force field design Kenno Vanommeslaeghe (Wed Jul 16 2014 - 12:24:29 CDT)
  - RE: Force field design Abhishek TYAGI (Sat Jul 19 2014 - 07:44:53 CDT)
    - Re: Force field design Kenno Vanommeslaeghe (Mon Jul 21 2014 - 10:47:12 CDT)
- RE: Force field design Abhishek TYAGI (Tue Jul 22 2014 - 05:40:00 CDT)
  - Re: Force field design Mayne, Christopher G (Tue Jul 22 2014 - 09:01:58 CDT)
NADH topology file Kevin C Chan (Tue Jul 15 2014 - 05:41:51 CDT)
- Re: NADH topology file Kenno Vanommeslaeghe (Tue Jul 15 2014 - 09:44:10 CDT)
- Re: NADH topology file Kevin C Chan (Wed Jul 16 2014 - 01:51:22 CDT)
  - Re: Re: NADH topology file Kenno Vanommeslaeghe (Wed Jul 16 2014 - 12:39:02 CDT)
Fwd: Re: Branko (Mon Jul 14 2014 - 13:24:43 CDT)
(no subject) Eifler, Jay Q. (UMKC-Student) (Mon Jul 14 2014 - 13:05:36 CDT)
- Re: Aron Broom (Mon Jul 14 2014 - 13:18:14 CDT)
- Re: Gianluca Interlandi (Mon Jul 14 2014 - 13:26:57 CDT)
- Re: Kenno Vanommeslaeghe (Mon Jul 14 2014 - 15:58:25 CDT)
Re: Regarding Temperature calculation from velocity trajectory of NAMD-2.9 Shailesh Pandey (Fri Jul 11 2014 - 06:14:59 CDT)
AW: Regarding Temperature calculation from velocity trajectory of NAMD-2.9 Norman Geist (Fri Jul 11 2014 - 02:51:44 CDT)
Regarding free energy cost incurred by using pseudo bonds Sharmon (Thu Jul 10 2014 - 13:29:29 CDT)
variable force constant Lu Hong (Thu Jul 10 2014 - 12:34:58 CDT)
- Re: variable force constant Aron Broom (Thu Jul 10 2014 - 13:00:32 CDT)
Fwd: Regarding Temperature calculation from velocity trajectory of NAMD-2.9 Shailesh Pandey (Thu Jul 10 2014 - 09:31:03 CDT)
Regarding Temperature calculation from velocity trajectory of NAMD-2.9 Shailesh Pandey (Thu Jul 10 2014 - 04:30:20 CDT)
- AW: Regarding Temperature calculation from velocity trajectory of NAMD-2.9 Norman Geist (Thu Jul 10 2014 - 05:08:50 CDT)
parameter and topology files for martini polarizable water Klas Karis (Wed Jul 09 2014 - 18:30:23 CDT)
- Re: parameter and topology files for martini polarizable water Fotis Baltoumas (Thu Jul 10 2014 - 04:17:31 CDT)
  - Re: parameter and topology files for martini polarizable water Klas Karis (Thu Jul 10 2014 - 12:11:35 CDT)
accelerated MD as the engine for loop refirement James Starlight (Wed Jul 09 2014 - 14:39:08 CDT)
- Re: accelerated MD as the engine for loop refirement Gianluca Interlandi (Wed Jul 09 2014 - 15:08:17 CDT)
  - Re: accelerated MD as the engine for loop refirement Kenno Vanommeslaeghe (Thu Jul 10 2014 - 17:32:38 CDT)
- Re: accelerated MD as the engine for loop refirement Ajasja LjubetiÄ (Wed Jul 09 2014 - 15:22:15 CDT)
  - Re: accelerated MD as the engine for loop refirement James Starlight (Thu Jul 10 2014 - 04:39:17 CDT)
how to quantify and visualize the flow of water into a protein Thomas Evangelidis (Tue Jul 08 2014 - 18:20:48 CDT)
- Re: how to quantify and visualize the flow of water into a protein Maxim Belkin (Tue Jul 08 2014 - 18:40:15 CDT)
  - Re: how to quantify and visualize the flow of water into a protein Thomas Evangelidis (Tue Jul 08 2014 - 19:04:01 CDT)
- Re: how to quantify and visualize the flow of water into a protein Joshua Adelman (Tue Jul 08 2014 - 19:36:02 CDT)
Bad global crossterm count! Mitul Saha (Tue Jul 08 2014 - 16:46:17 CDT)
- Re: Bad global crossterm count! Mitul Saha (Tue Jul 08 2014 - 16:48:51 CDT)
About asterisk in IC statements in topology files Kevin C Chan (Tue Jul 08 2014 - 02:30:25 CDT)
Hexagonal cell instability during lipid bilayer sim in NAMD 2.9 Michael Bokoch (Mon Jul 07 2014 - 21:42:54 CDT)
NAMD energy plugin - dielectric constant Ramin Ekhteiari (Mon Jul 07 2014 - 14:59:42 CDT)
(no subject) sudipta.mml (Mon Jul 07 2014 - 01:08:12 CDT)
Regarding NAMD and MD simulations Joel Moniz (Mon Jul 07 2014 - 01:42:04 CDT)
- AW: Regarding NAMD and MD simulations Norman Geist (Mon Jul 07 2014 - 02:48:08 CDT)
  - Re: AW: Regarding NAMD and MD simulations Joel Moniz (Tue Jul 08 2014 - 22:17:19 CDT)
two O atoms in CTER are unusually close Fulu Zheng (Sat Jul 05 2014 - 02:05:28 CDT)
- Re: two O atoms in CTER are unusually close Kenno Vanommeslaeghe (Thu Jul 10 2014 - 17:28:08 CDT)
Nanotube tutorial Adam Kells (Fri Jul 04 2014 - 13:19:33 CDT)
(no subject) zmhoseyni (Thu Jul 03 2014 - 22:36:44 CDT)
PMF calculations between membrane and nano particle simulations Subbarao Kanchi (Thu Jul 03 2014 - 15:58:23 CDT)
- Re: PMF calculations between membrane and nano particle simulations Giacomo Fiorin (Thu Jul 03 2014 - 16:34:33 CDT)
  - Re: PMF calculations between membrane and nano particle simulations Subbarao Kanchi (Thu Jul 03 2014 - 17:46:24 CDT)
    - Re: PMF calculations between membrane and nano particle simulations Giacomo Fiorin (Mon Jul 07 2014 - 18:05:06 CDT)
    - Re: PMF calculations between membrane and nano particle simulations Subbarao Kanchi (Tue Jul 08 2014 - 01:01:15 CDT)
Re: REMD on IBM iDataPlex DX360M3 Francesco Pietra (Thu Jul 03 2014 - 04:53:32 CDT)
- AW: REMD on IBM iDataPlex DX360M3 Norman Geist (Thu Jul 03 2014 - 05:38:48 CDT)
- AW: REMD on IBM iDataPlex DX360M3 Norman Geist (Thu Jul 03 2014 - 05:42:02 CDT)
- Re: REMD on IBM iDataPlex DX360M3 Francesco Pietra (Thu Jul 03 2014 - 09:42:41 CDT)
  - Fwd: REMD on IBM iDataPlex DX360M3 Francesco Pietra (Tue Jul 08 2014 - 00:41:54 CDT)
    - AW: REMD on IBM iDataPlex DX360M3 Norman Geist (Tue Jul 08 2014 - 01:12:46 CDT)
- Re: REMD on IBM iDataPlex DX360M3 Francesco Pietra (Tue Jul 08 2014 - 12:14:10 CDT)
  - AW: REMD on IBM iDataPlex DX360M3 Norman Geist (Wed Jul 09 2014 - 02:24:27 CDT)
REMD on IBM iDataPlex DX360M3 Francesco Pietra (Thu Jul 03 2014 - 01:15:21 CDT)
- AW: REMD on IBM iDataPlex DX360M3 Norman Geist (Thu Jul 03 2014 - 04:28:46 CDT)
namd-slurm file Ramin Ekhteiari (Wed Jul 02 2014 - 10:08:31 CDT)
(no subject) zmhoseyni (Wed Jul 02 2014 - 00:25:31 CDT)
Invalid command error Adam Kells (Mon Jun 30 2014 - 06:49:07 CDT)
- Re: Invalid command error Axel Kohlmeyer (Mon Jun 30 2014 - 07:44:41 CDT)
calculating free energy Alireza Mansouri (Sat Jun 28 2014 - 12:22:40 CDT)
- Re: calculating free energy Aron Broom (Sat Jun 28 2014 - 15:53:02 CDT)
Invitation to Submit Review Article Current Protein & Peptide Science (IF: 2.326) Prija Ponnan (Fri Jun 27 2014 - 06:40:43 CDT)
Namd grid forces -distance between molecule and surface Mohan maruthi sena (Fri Jun 27 2014 - 05:20:29 CDT)
Restraints between ion and small molecule Daniel Torrente (Thu Jun 26 2014 - 11:53:49 CDT)
- Re: Restraints between ion and small molecule Kenno Vanommeslaeghe (Thu Jun 26 2014 - 13:16:31 CDT)
Re: NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation?? Shailesh Pandey (Thu Jun 26 2014 - 04:41:49 CDT)
- Re: NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation?? Ivan Gregoretti (Thu Jun 26 2014 - 08:34:16 CDT)
NAMD energy calculation Ramin Ekhteiari (Wed Jun 25 2014 - 11:45:33 CDT)
- Re: vmd-l: NAMD energy calculation John Stone (Mon Jun 30 2014 - 22:59:28 CDT)
  - RE: Re: vmd-l: NAMD energy calculation Morgan, Brittany (Tue Jul 01 2014 - 09:26:44 CDT)
    - Re: Re: vmd-l: NAMD energy calculation Ramin Ekhteiari (Tue Jul 01 2014 - 12:07:47 CDT)
    - RE: Re: vmd-l: NAMD energy calculation Morgan, Brittany (Wed Jul 02 2014 - 11:58:22 CDT)
PMF and work distribution Mustafa Tekpinar (Wed Jun 25 2014 - 05:50:30 CDT)
- Re: PMF and work distribution Giacomo Fiorin (Wed Jun 25 2014 - 12:12:52 CDT)
  - Re: PMF and work distribution Ajasja LjubetiÄ (Thu Jun 26 2014 - 08:05:48 CDT)
Xeon vs i7 and ECC vs SDRAM Gianluca Interlandi (Tue Jun 24 2014 - 20:02:49 CDT)
- Re: Xeon vs i7 and ECC vs SDRAM Gianluca Interlandi (Tue Jun 24 2014 - 23:07:02 CDT)
- AW: Xeon vs i7 and ECC vs SDRAM Norman Geist (Wed Jun 25 2014 - 00:31:47 CDT)
  - Re: AW: Xeon vs i7 and ECC vs SDRAM Gianluca Interlandi (Wed Jun 25 2014 - 01:14:48 CDT)
    - AW: AW: Xeon vs i7 and ECC vs SDRAM Norman Geist (Wed Jun 25 2014 - 01:47:38 CDT)
  - Re: AW: Xeon vs i7 and ECC vs SDRAM Kenno Vanommeslaeghe (Wed Jun 25 2014 - 10:26:26 CDT)
    - AW: AW: Xeon vs i7 and ECC vs SDRAM Norman Geist (Thu Jun 26 2014 - 00:59:13 CDT)
How to apply a magnetic field with NAMD Faezeh Mottaghitalab (Tue Jun 24 2014 - 16:00:48 CDT)
- Re: How to apply a magnetic field with NAMD Ajasja LjubetiÄ (Tue Jun 24 2014 - 16:52:06 CDT)
  - Re: How to apply a magnetic field with NAMD Axel Kohlmeyer (Tue Jun 24 2014 - 19:43:42 CDT)
    - Re: How to apply a magnetic field with NAMD Kenno Vanommeslaeghe (Wed Jun 25 2014 - 10:08:11 CDT)
    - Re: How to apply a magnetic field with NAMD Faezeh Mottaghitalab (Wed Jun 25 2014 - 15:40:43 CDT)
paricle type in residue based coarse graining of NAMD Yongcheng Zhou (Mon Jun 23 2014 - 09:14:12 CDT)
- AW: paricle type in residue based coarse graining of NAMD Norman Geist (Tue Jun 24 2014 - 03:13:21 CDT)
paricle type in residue based coarse graining of NAMD Yongcheng Zhou (Mon Jun 23 2014 - 14:37:16 CDT)
Fatal error.. Gurpreet Kaur Dhindsa (Sun Jun 22 2014 - 17:32:16 CDT)
- AW: Fatal error.. Norman Geist (Mon Jun 23 2014 - 03:33:27 CDT)
memory problem Adam Moser (Fri Jun 20 2014 - 15:01:30 CDT)
NAMD on CRAY XE6m-200: dynamic linking in tcl not working Harish Vashisth (Fri Jun 20 2014 - 14:07:31 CDT)
- Re: NAMD on CRAY XE6m-200: dynamic linking in tcl not working Axel Kohlmeyer (Fri Jun 20 2014 - 14:36:37 CDT)
  - Re: NAMD on CRAY XE6m-200: dynamic linking in tcl not working Harish Vashisth (Fri Jun 20 2014 - 15:17:34 CDT)
  - Re: NAMD on CRAY XE6m-200: dynamic linking in tcl not working Harish Vashisth (Fri Jun 20 2014 - 18:49:59 CDT)
Unsubscribe jafar azamat (Fri Jun 20 2014 - 03:27:10 CDT)
ffTK and phase angles Benjamin Hill (Thu Jun 19 2014 - 17:43:28 CDT)
- Re: ffTK and phase angles Kenno Vanommeslaeghe (Thu Jun 19 2014 - 20:01:05 CDT)
Subject: Re:Re: New partial charges after patching Sadegh Faramarzi Ganjabad (Thu Jun 19 2014 - 03:21:33 CDT)
- Re: Subject: Re:Re: New partial charges after patching Kenno Vanommeslaeghe (Thu Jun 19 2014 - 10:11:28 CDT)
  - Re: Subject: Re:Re: New partial charges after patching Kenno Vanommeslaeghe (Fri Jul 11 2014 - 12:19:21 CDT)
Unsubscribe Dhanashree Khanale (Thu Jun 19 2014 - 03:19:51 CDT)
Should PME be used for electrostatic interaction energy calculations? Fotis Baltoumas (Wed Jun 18 2014 - 12:59:16 CDT)
- AW: Should PME be used for electrostatic interaction energy calculations? Norman Geist (Thu Jun 19 2014 - 02:25:49 CDT)
- Re: Should PME be used for electrostatic interaction energy calculations? Thomas Evangelidis (Thu Jun 19 2014 - 02:38:50 CDT)
- AW: Should PME be used for electrostatic interaction energy calculations? Norman Geist (Thu Jun 19 2014 - 02:46:48 CDT)
Constraint failure in RATTLE algorithm Douglas Houston (Wed Jun 18 2014 - 12:29:48 CDT)
- Re: Constraint failure in RATTLE algorithm Axel Kohlmeyer (Wed Jun 18 2014 - 13:23:05 CDT)
  - Re: Constraint failure in RATTLE algorithm Aron Broom (Wed Jun 18 2014 - 14:07:04 CDT)
    - RE: Constraint failure in RATTLE algorithm Tristan Croll (Wed Jun 18 2014 - 20:29:08 CDT)
    - AW: Constraint failure in RATTLE algorithm Norman Geist (Thu Jun 19 2014 - 02:29:16 CDT)
  - Re: Constraint failure in RATTLE algorithm Douglas Houston (Thu Jun 19 2014 - 05:26:53 CDT)
is the aMD implementation compatible with AMBER force fields Thomas Evangelidis (Wed Jun 18 2014 - 06:20:06 CDT)
- Re: is the aMD implementation compatible with AMBER force fields Jeff Wereszczynski (Wed Jun 18 2014 - 13:14:11 CDT)
  - Re: is the aMD implementation compatible with AMBER force fields Thomas Evangelidis (Wed Jun 18 2014 - 18:20:00 CDT)
Inquiry about lipid membrane simulation Mo Chen (Tue Jun 17 2014 - 20:57:59 CDT)
- Re: Inquiry about lipid membrane simulation Kenno Vanommeslaeghe (Wed Jun 18 2014 - 10:20:24 CDT)
  - Re: Inquiry about lipid membrane simulation Kenno Vanommeslaeghe (Wed Jun 18 2014 - 14:02:52 CDT)
Merging the two files...... Gurpreet Kaur Dhindsa (Tue Jun 17 2014 - 10:00:09 CDT)
- Re: Merging the two files...... Aron Broom (Tue Jun 17 2014 - 10:44:36 CDT)
  - Re: Merging the two files...... Aron Broom (Tue Jun 17 2014 - 10:58:22 CDT)
    - Algorithm used by NAMD Gurpreet Kaur Dhindsa (Thu Apr 02 2015 - 09:55:36 CDT)
    - Re: Algorithm used by NAMD David Hardy (Fri Apr 03 2015 - 11:18:46 CDT)
Reg : MD simulation with DMSO instead of water Akshay Bhatnagar (Tue Jun 17 2014 - 06:04:58 CDT)
- Re: Reg : MD simulation with DMSO instead of water Axel Kohlmeyer (Tue Jun 17 2014 - 06:12:55 CDT)
  - Re: Reg : MD simulation with DMSO instead of water Kenno Vanommeslaeghe (Tue Jun 17 2014 - 13:13:02 CDT)
alchemical free energy simulations with parmtop Hannes Loeffler (Tue Jun 17 2014 - 04:35:59 CDT)
- Re: alchemical free energy simulations with parmtop Hannes Loeffler (Mon Dec 01 2014 - 03:20:17 CST)
  - Re: Re: alchemical free energy simulations with parmtop Jim Phillips (Tue Dec 02 2014 - 12:06:40 CST)
improving tclforce efficiency, getting "Signal: segmentation violation" error zeynab mohamad hoseyni (Sun Jun 15 2014 - 20:18:11 CDT)
unsubscribe Laura (Sun Jun 15 2014 - 12:29:39 CDT)
The short range nonbonbed force charge after load balancing Â¬Óíï¿ (Sun Jun 15 2014 - 04:57:43 CDT)
New partial charges after patching Sadegh Faramarzi Ganjabad (Sat Jun 14 2014 - 04:15:47 CDT)
- Re: New partial charges after patching Kenno Vanommeslaeghe (Mon Jun 16 2014 - 10:23:02 CDT)
About converting NAMD dcd file into CHARMM dcd file Mo Chen (Fri Jun 13 2014 - 18:41:30 CDT)
- Re: About converting NAMD dcd file into CHARMM dcd file Kenno Vanommeslaeghe (Fri Jun 13 2014 - 21:18:52 CDT)
Re: AW: Using nodelist file causes namd to hang Douglas Houston (Fri Jun 13 2014 - 12:17:15 CDT)
- AW: AW: Using nodelist file causes namd to hang Norman Geist (Mon Jun 16 2014 - 02:19:28 CDT)
  - Re: AW: AW: Using nodelist file causes namd to hang Douglas Houston (Wed Jun 18 2014 - 07:24:00 CDT)
AW: Reg: movement of protein outside box Norman Geist (Fri Jun 13 2014 - 03:09:20 CDT)
How to refer to side-chain via tcl-force scripting? zeynab mohamad hoseyni (Fri Jun 13 2014 - 00:53:12 CDT)
- RE: How to refer to side-chain via tcl-force scripting? Tristan Croll (Fri Jun 13 2014 - 02:08:51 CDT)
- AW: How to refer to side-chain via tcl-force scripting? Norman Geist (Fri Jun 13 2014 - 02:53:41 CDT)
- AW: How to refer to side-chain via tcl-force scripting? Norman Geist (Fri Jun 13 2014 - 02:56:03 CDT)
  - Re: AW: How to refer to side-chain via tcl-force scripting? zeynab mohamad hoseyni (Fri Jun 13 2014 - 03:21:08 CDT)
NAMD_2.9_Linux-x86_64-multicore-CUDA Segfaults Vlastimil ZÃma (Wed Jun 11 2014 - 02:36:44 CDT)
- Re: NAMD_2.9_Linux-x86_64-multicore-CUDA Segfaults Axel Kohlmeyer (Wed Jun 11 2014 - 02:42:48 CDT)
  - Re: NAMD_2.9_Linux-x86_64-multicore-CUDA Segfaults Axel Kohlmeyer (Wed Jun 11 2014 - 03:13:56 CDT)
- AW: NAMD_2.9_Linux-x86_64-multicore-CUDA Segfaults Norman Geist (Wed Jun 11 2014 - 03:07:21 CDT)
AW: Reg: movement of protein outside box Norman Geist (Tue Jun 10 2014 - 07:26:58 CDT)
Reg: movement of protein outside box Akshay Bhatnagar (Mon Jun 09 2014 - 20:46:56 CDT)
- Re: Reg: movement of protein outside box Aron Broom (Mon Jun 09 2014 - 22:09:28 CDT)
- AW: Reg: movement of protein outside box Norman Geist (Tue Jun 10 2014 - 02:47:32 CDT)
NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation?? Shailesh Pandey (Mon Jun 09 2014 - 12:54:03 CDT)
- AW: NAMD-2.9:Help needed on how to write to different DCD files in a single running NAMD simulation?? Norman Geist (Tue Jun 10 2014 - 02:43:11 CDT)
boron nitride nanotube Z (Mon Jun 09 2014 - 02:58:02 CDT)
- Re: boron nitride nanotube Axel Kohlmeyer (Mon Jun 09 2014 - 04:19:24 CDT)
  - Re: boron nitride nanotube Z (Thu Jun 12 2014 - 05:28:33 CDT)
    - Re: boron nitride nanotube Axel Kohlmeyer (Thu Jun 12 2014 - 05:46:33 CDT)
change in pdb.. Gurpreet Kaur Dhindsa (Sat Jun 07 2014 - 18:37:41 CDT)
- change in pdb.. Gurpreet Kaur Dhindsa (Wed Jun 11 2014 - 09:39:31 CDT)
  - Re: change in pdb.. Ivan Gregoretti (Wed Jun 11 2014 - 10:29:05 CDT)
NAMD Multicore CUDA usage Ravi Abrol (Fri Jun 06 2014 - 14:20:10 CDT)
- AW: NAMD Multicore CUDA usage Norman Geist (Tue Jun 10 2014 - 02:33:13 CDT)
alchElecLambdaStart (Thermodynamic Integration) Javad Noroozi (Fri Jun 06 2014 - 13:55:28 CDT)
Reg: deformation of water box during equilibration Akshay Bhatnagar (Fri Jun 06 2014 - 11:35:34 CDT)
- Re: Reg: deformation of water box during equilibration Aron Broom (Fri Jun 06 2014 - 12:37:30 CDT)
  - Re: Reg: deformation of water box during equilibration Akshay Bhatnagar (Fri Jun 06 2014 - 21:15:30 CDT)
Fixed atoms. Gurpreet Kaur Dhindsa (Thu Jun 05 2014 - 16:15:05 CDT)
- Re: Fixed atoms. Aron Broom (Thu Jun 05 2014 - 17:03:12 CDT)
  - Re: Fixed atoms. Maxim Belkin (Thu Jun 05 2014 - 17:14:48 CDT)
NAMD energy plugin Ramin Ekhteiari (Wed Jun 04 2014 - 12:45:36 CDT)
- Re: NAMD energy plugin Aron Broom (Wed Jun 04 2014 - 13:34:51 CDT)
  - Re: NAMD energy plugin Ramin Ekhteiari (Wed Jun 04 2014 - 13:55:23 CDT)
    - Re: NAMD energy plugin Kenno Vanommeslaeghe (Wed Jun 04 2014 - 14:16:48 CDT)
  - Re: NAMD energy plugin Kenno Vanommeslaeghe (Wed Jun 04 2014 - 14:10:39 CDT)
    - Re: NAMD energy plugin MEHRAN MB (Wed Jun 04 2014 - 15:16:09 CDT)
non-neutralized system Research Jubilant (Wed Jun 04 2014 - 10:29:47 CDT)
Ion Au+3 simulation Daniel Torrente (Tue Jun 03 2014 - 13:31:40 CDT)
- Re: Ion Au+3 simulation Axel Kohlmeyer (Tue Jun 03 2014 - 14:38:35 CDT)
  - Re: Ion Au+3 simulation Daniel Torrente (Tue Jun 03 2014 - 15:17:15 CDT)
Density of water box Akshay Bhatnagar (Tue Jun 03 2014 - 05:22:00 CDT)
- Re: Density of water box Ana Celia Vila Verde (Tue Jun 03 2014 - 06:29:02 CDT)
  - Re: Density of water box Akshay Bhatnagar (Tue Jun 03 2014 - 07:26:41 CDT)
coordinates in namd Research Jubilant (Mon Jun 02 2014 - 23:34:52 CDT)
- AW: coordinates in namd Norman Geist (Tue Jun 03 2014 - 01:40:14 CDT)
- RE: coordinates in namd Tristan Croll (Tue Jun 03 2014 - 02:25:49 CDT)
About electrostatic treatment Mo Chen (Fri May 30 2014 - 19:35:50 CDT)
- Re: About electrostatic treatment Mo Chen (Fri May 30 2014 - 19:39:31 CDT)
- Re: About electrostatic treatment David Hardy (Sat May 31 2014 - 12:01:34 CDT)
code implementation based on NAMD source code Teerapong Pirojsirikul (Thu May 29 2014 - 17:39:21 CDT)
FEP of water molecule in binding pocket Monika Sharma (Wed May 28 2014 - 15:35:33 CDT)
Rapid and accurate parameterization of new molecules in CHARMM Aaron Larsen (Tue May 27 2014 - 08:21:06 CDT)
- RE: Rapid and accurate parameterization of new molecules in CHARMM JC Gumbart (Tue May 27 2014 - 09:19:40 CDT)
  - RE: Rapid and accurate parameterization of new molecules in CHARMM Tristan Croll (Tue May 27 2014 - 17:23:07 CDT)
  - Re: Rapid and accurate parameterization of new molecules in CHARMM Kenno Vanommeslaeghe (Tue May 27 2014 - 17:58:42 CDT)
    - Re: Rapid and accurate parameterization of new molecules in CHARMM Aaron Larsen (Tue May 27 2014 - 19:22:22 CDT)
    - Re: Rapid and accurate parameterization of new molecules in CHARMM Kenno Vanommeslaeghe (Wed May 28 2014 - 10:35:07 CDT)
constraint file from amber prmtop/inpcrd amin_at_imtech.res.in (Sat May 24 2014 - 14:32:55 CDT)
IMPROPER PARAMETERS FOR CA CA CA CA Z (Sat May 24 2014 - 10:50:49 CDT)
- Re: IMPROPER PARAMETERS FOR CA CA CA CA Kenno Vanommeslaeghe (Mon May 26 2014 - 16:42:29 CDT)
  - Re: IMPROPER PARAMETERS FOR CA CA CA CA Axel Kohlmeyer (Mon May 26 2014 - 16:47:44 CDT)
*** glibc detected *** namd2: invalid fastbin entry (free) Wesley Lay (Thu May 22 2014 - 15:19:11 CDT)
(no subject) zmhoseyni (Wed May 21 2014 - 04:48:25 CDT)
building namd on a Cray XE6 with Interlagos procs Giovanni Settanni (Tue May 20 2014 - 09:03:22 CDT)
(no subject) zmhoseyni (Mon May 19 2014 - 04:18:48 CDT)
COLVAR metadynamics: center of mass of atoms crossing simulation box Lorenz Ripka (Mon May 19 2014 - 03:44:36 CDT)
- COLVAR metadynamics: center of mass of atoms crossing simulation box Lorenz Ripka (Mon May 19 2014 - 07:17:47 CDT)
  - Re: COLVAR metadynamics: center of mass of atoms crossing simulation box Giacomo Fiorin (Tue May 20 2014 - 11:41:56 CDT)
    - Re: COLVAR metadynamics: center of mass of atoms crossing simulation box Lorenz Ripka (Fri May 23 2014 - 07:35:23 CDT)
Re: Steered MD with the RMSD colvar George Patargias (Mon May 19 2014 - 05:01:12 CDT)
- Re: Steered MD with the RMSD colvar Giacomo Fiorin (Wed May 21 2014 - 17:52:54 CDT)
  - Re: Steered MD with the RMSD colvar George Patargias (Thu Jul 03 2014 - 06:26:19 CDT)
Workshop on Very Large System Simulation Workshop, Urbana, IL, August 11-15, 2014 David Brandon (Sat May 17 2014 - 18:22:07 CDT)
running Multiple-replicas metadynamics Osvalds Verners (Fri May 16 2014 - 13:01:08 CDT)
- Re: running Multiple-replicas metadynamics Giacomo Fiorin (Fri May 16 2014 - 14:00:41 CDT)
  - Re: running Multiple-replicas metadynamics Osvalds Verners (Fri May 16 2014 - 14:21:28 CDT)
Polymer Layer/ Cutoff Rawan Al Nsour (Thu May 15 2014 - 11:19:21 CDT)
- Re: Polymer Layer/ Cutoff Kenno Vanommeslaeghe (Thu May 15 2014 - 11:58:43 CDT)
  - Re: Polymer Layer/ Cutoff Kenno Vanommeslaeghe (Thu May 15 2014 - 14:34:00 CDT)
    - Re: Polymer Layer/ Cutoff Rawan Al Nsour (Thu May 15 2014 - 16:13:58 CDT)
    - Re: Polymer Layer/ Cutoff Kenno Vanommeslaeghe (Thu May 15 2014 - 18:00:42 CDT)
NAMD-GPU Ramin Ekhteiari (Wed May 14 2014 - 07:19:10 CDT)
- Re: NAMD-GPU Axel Kohlmeyer (Wed May 14 2014 - 07:51:37 CDT)
  - Re: NAMD-GPU Aron Broom (Wed May 14 2014 - 09:54:20 CDT)
Scaling solvent-solute intermolecular interactions Michael Bellucci (Tue May 13 2014 - 13:34:13 CDT)
- Re: Scaling solvent-solute intermolecular interactions Axel Kohlmeyer (Tue May 13 2014 - 13:56:02 CDT)
  - RE: Scaling solvent-solute intermolecular interactions Michael Bellucci (Tue May 13 2014 - 15:09:06 CDT)
NAMD-SMP-Ibverbs-CUDA assistance Matthew Ralph Adendorff (Tue May 13 2014 - 09:25:44 CDT)
- AW: NAMD-SMP-Ibverbs-CUDA assistance Norman Geist (Wed May 14 2014 - 00:42:51 CDT)
Dual boost accelerated md energy parameters? Per Larsson (Mon May 12 2014 - 13:54:48 CDT)
- Re: Dual boost accelerated md energy parameters? Thomas Evangelidis (Mon May 12 2014 - 14:11:45 CDT)
unsubscribe Shalton Evans (Sun May 11 2014 - 19:18:39 CDT)
Protein solvation farzad kiani (Sat May 10 2014 - 12:28:26 CDT)
- Re: Protein solvation Kipp Johnson (Sat May 10 2014 - 15:38:26 CDT)
FixedAtoms and Reference group in spinangle colvar nicolas martin (Fri May 09 2014 - 09:01:28 CDT)
- Re: FixedAtoms and Reference group in spinangle colvar JÃ©rÃ´me HÃ©nin (Fri May 09 2014 - 13:53:56 CDT)
  - Re: FixedAtoms and Reference group in spinangle colvar nicolas martin (Sun May 11 2014 - 16:52:42 CDT)
error while making psf file for bacteriorhodopsin system Faezeh Mottaghitalab (Thu May 08 2014 - 15:11:26 CDT)
- Re: error while making psf file for bacteriorhodopsin system Kenno Vanommeslaeghe (Thu May 08 2014 - 15:57:52 CDT)
  - Re: error while making psf file for bacteriorhodopsin system Kenno Vanommeslaeghe (Fri May 09 2014 - 11:38:08 CDT)
    - Re: error while making psf file for bacteriorhodopsin system Faezeh Mottaghitalab (Fri May 09 2014 - 13:10:55 CDT)
PMF from ABF simulation not plateauing Riley Workman (Thu May 08 2014 - 12:08:13 CDT)
- Re: PMF from ABF simulation not plateauing Aron Broom (Thu May 08 2014 - 13:56:37 CDT)
- Re: PMF from ABF simulation not plateauing JÃ©rÃ´me HÃ©nin (Thu May 08 2014 - 17:37:20 CDT)
Setting up membrane protein simulation from existing conformation? Per Larsson (Wed May 07 2014 - 14:17:41 CDT)
- Re: Setting up membrane protein simulation from existing conformation? Kenno Vanommeslaeghe (Wed May 07 2014 - 14:44:00 CDT)
  - Re: Setting up membrane protein simulation from existing conformation? Per Larsson (Wed May 07 2014 - 15:12:53 CDT)
NAMD and NUMA Joseph Farran (Wed May 07 2014 - 13:54:51 CDT)
- AW: NAMD and NUMA Norman Geist (Thu May 08 2014 - 01:53:12 CDT)
  - Re: AW: NAMD and NUMA Joseph Farran (Thu May 08 2014 - 11:28:46 CDT)
  - Re: AW: NAMD and NUMA Joseph Farran (Thu May 08 2014 - 11:33:25 CDT)
choose the best equilibrium arrangement of water molecules Boshra Moradi (Tue May 06 2014 - 16:55:17 CDT)
(no subject) Boshra Moradi (Tue May 06 2014 - 16:35:44 CDT)
TclForces wrapmode FATAL ERROR: Setting parameter wrapmode from script failed Norman Geist (Tue May 06 2014 - 05:49:45 CDT)
- Re: TclForces wrapmode FATAL ERROR: Setting parameter wrapmode from script failed Maxim Belkin (Wed May 07 2014 - 16:15:22 CDT)
  - AW: TclForces wrapmode FATAL ERROR: Setting parameter wrapmode from script failed Norman Geist (Thu May 08 2014 - 01:54:10 CDT)
Topology for lysine bouding in Epsilon Jean-Patrick Francoia (Mon May 05 2014 - 12:11:23 CDT)
- Re: Topology for lysine bouding in Epsilon Kenno Vanommeslaeghe (Mon May 05 2014 - 15:07:31 CDT)
  - Re: Topology for lysine bouding in Epsilon Kenno Vanommeslaeghe (Tue May 06 2014 - 13:06:38 CDT)
Colvars keyword problem Sofya Lushchekina (Mon May 05 2014 - 09:32:11 CDT)
- Re: Colvars keyword problem JÃ©rÃ´me HÃ©nin (Mon May 05 2014 - 10:01:03 CDT)
Empirical force fields: release new version of RED Server Dev/PyRED FyD (Mon May 05 2014 - 06:07:18 CDT)
Force field for sulfated tyrosines Shaon Chakrabarti (Sun May 04 2014 - 21:35:38 CDT)
- Re: Force field for sulfated tyrosines Kenno Vanommeslaeghe (Mon May 05 2014 - 13:11:47 CDT)
Patch to connect monomers code Rawan Al Nsour (Sun May 04 2014 - 12:15:12 CDT)
- Re: Patch to connect monomers code Kenno Vanommeslaeghe (Mon May 05 2014 - 13:11:36 CDT)
  - Re: Patch to connect monomers code Kenno Vanommeslaeghe (Tue May 06 2014 - 13:33:49 CDT)
Getting extra atoms by Patching! Sadegh Faramarzi Ganjabad (Fri May 02 2014 - 18:51:31 CDT)
- Re: Getting extra atoms by Patching! Michelle Kuttel (Sat May 03 2014 - 01:11:50 CDT)
  - Re: Getting extra atoms by Patching! Kenno Vanommeslaeghe (Mon May 05 2014 - 11:45:48 CDT)
  - Re: Getting extra atoms by Patching! Kenno Vanommeslaeghe (Thu May 08 2014 - 12:38:10 CDT)
    - Fwd: Getting extra atoms by Patching! Sadegh Faramarzi Ganjabad (Thu May 08 2014 - 15:49:14 CDT)
Re: Teflon New Residue Rawan Al Nsour (Fri May 02 2014 - 11:10:38 CDT)
- Re: Teflon New Residue Kenno Vanommeslaeghe (Fri May 02 2014 - 12:21:09 CDT)
Teflon New Residue Rawan Al Nsour (Fri May 02 2014 - 09:57:57 CDT)
How to extract the .coor, .vel and .xsc files for a conformation in the middle of trajectory zeynab mohamad hoseyni (Mon Apr 28 2014 - 23:12:57 CDT)
- AW: How to extract the .coor, .vel and .xsc files for a conformation in the middle of trajectory Norman Geist (Tue Apr 29 2014 - 02:20:33 CDT)
- AW: How to extract the .coor, .vel and .xsc files for a conformation in the middle of trajectory Norman Geist (Tue Apr 29 2014 - 02:21:20 CDT)
FEP is in kj/mol Javad Noroozi (Sun Apr 27 2014 - 08:32:33 CDT)
Using the CHARMM36 forcefield with NAMD Alex Utev (CMP) (Wed Apr 23 2014 - 11:15:08 CDT)
- Re: Using the CHARMM36 forcefield with NAMD Kenno Vanommeslaeghe (Wed Apr 23 2014 - 12:28:33 CDT)
  - Re: Using the CHARMM36 forcefield with NAMD Kenno Vanommeslaeghe (Fri May 09 2014 - 11:50:45 CDT)
FATAL ERROR: Setting parameter tclForces from script failed! zeynab mohamad hoseyni (Tue Apr 22 2014 - 02:43:23 CDT)
TI analysis script Javad Noroozi (Sat Apr 19 2014 - 08:16:18 CDT)
Workshop on GPU Programming for Molecular Modeling, in Urbana, Illinois, July 22-24, 2014 David Brandon (Fri Apr 18 2014 - 16:49:02 CDT)
Collective Variables to Restrain Ions Away From Protein Chris Ing (Thu Apr 17 2014 - 18:36:06 CDT)
- Re: Collective Variables to Restrain Ions Away From Protein Aron Broom (Thu Apr 17 2014 - 23:15:35 CDT)
  - Re: Collective Variables to Restrain Ions Away From Protein Aron Broom (Sun Apr 20 2014 - 00:27:37 CDT)
peptide tends to migrate out the water box Francesco Pietra (Thu Apr 17 2014 - 17:02:01 CDT)
- Re: peptide tends to migrate out the water box Ana Celia Vila Verde (Fri Apr 18 2014 - 02:12:40 CDT)
  - Re: peptide tends to migrate out the water box Francesco Pietra (Fri Apr 18 2014 - 03:14:49 CDT)
- Re: peptide tends to migrate out the water box Kenno Vanommeslaeghe (Fri Apr 18 2014 - 10:27:09 CDT)
CUDA error in cuda_check_local_progress Abhishek TYAGI (Thu Apr 17 2014 - 02:41:11 CDT)
- AW: CUDA error in cuda_check_local_progress Norman Geist (Thu Apr 17 2014 - 03:21:44 CDT)
  - RE: CUDA error in cuda_check_local_progress Abhishek TYAGI (Thu Apr 17 2014 - 04:07:36 CDT)
  - RE: CUDA error in cuda_check_local_progress Abhishek TYAGI (Thu Apr 17 2014 - 04:23:44 CDT)
    - AW: CUDA error in cuda_check_local_progress Norman Geist (Thu Apr 17 2014 - 04:50:10 CDT)
    - AW: CUDA error in cuda_check_local_progress Norman Geist (Tue Apr 22 2014 - 00:39:49 CDT)
How to setup a system with two pulling directions John Xi (Wed Apr 16 2014 - 19:32:27 CDT)
- Re: How to setup a system with two pulling directions Felipe Merino (Thu Apr 17 2014 - 10:38:06 CDT)
  - Re: How to setup a system with two pulling directions John Xi (Thu Apr 17 2014 - 19:48:39 CDT)
RBCG and NAMD 2.9 Raul Araya (Wed Apr 16 2014 - 13:21:43 CDT)
- Re: RBCG and NAMD 2.9 Ramya Gamini (Wed Apr 16 2014 - 14:49:54 CDT)
Step size in FEP calculation Javad Noroozi (Tue Apr 15 2014 - 23:21:35 CDT)
NAMD-Lite Hassan Kianinejad (Tue Apr 15 2014 - 17:22:56 CDT)
- Re: NAMD-Lite Axel Kohlmeyer (Tue Apr 15 2014 - 17:42:32 CDT)
  - Re: NAMD-Lite Axel Kohlmeyer (Tue Apr 15 2014 - 18:22:54 CDT)
- Re: NAMD-Lite Gianluca Interlandi (Tue Apr 15 2014 - 18:16:50 CDT)
Altering extrabonds forces during MD Bryan Roessler (Tue Apr 15 2014 - 09:53:02 CDT)
ABF with the RMSD colvar George Patargias (Tue Apr 15 2014 - 05:22:46 CDT)
- Re: ABF with the RMSD colvar Giacomo Fiorin (Tue Apr 15 2014 - 10:06:44 CDT)
(no subject) manish kesherwani (Tue Apr 15 2014 - 00:02:12 CDT)
- Re: Kenno Vanommeslaeghe (Tue Apr 15 2014 - 12:14:07 CDT)
  - Re: Aron Broom (Tue Apr 15 2014 - 13:47:48 CDT)
    - Re: manish kesherwani (Wed Apr 16 2014 - 13:21:34 CDT)
full electrostatics and pairlistdist Jonathan Phillips (Mon Apr 14 2014 - 16:25:04 CDT)
- Re: full electrostatics and pairlistdist Jason Swails (Wed Apr 16 2014 - 08:27:34 CDT)
  - Re: full electrostatics and pairlistdist Jonathan Phillips (Fri Apr 18 2014 - 05:51:02 CDT)
FEP error using CUDA Sadegh Faramarzi Ganjabad (Sun Apr 13 2014 - 22:42:12 CDT)
- Re: FEP error using CUDA Gianluca Interlandi (Sun Apr 13 2014 - 23:14:03 CDT)
Simulation crash during NPT equilibration James Starlight (Fri Apr 11 2014 - 05:58:17 CDT)
- AW: Simulation crash during NPT equilibration Norman Geist (Fri Apr 11 2014 - 06:31:49 CDT)
Nanotube Simulation Miro Hodak (Thu Apr 10 2014 - 18:02:56 CDT)
- Re: Nanotube Simulation Axel Kohlmeyer (Fri Apr 11 2014 - 03:36:44 CDT)
  - Re: Nanotube Simulation Miro Hodak (Fri Apr 11 2014 - 11:56:59 CDT)
Accelerated MD with transmembrane protein Kevin Kastner (Thu Apr 10 2014 - 13:40:26 CDT)
- Re: Accelerated MD with transmembrane protein Felipe Merino (Fri Apr 11 2014 - 03:27:09 CDT)
  - Re: Accelerated MD with transmembrane protein Jeff Wereszczynski (Fri Apr 11 2014 - 07:19:20 CDT)
Collective variable module naresh kumar (Thu Apr 10 2014 - 11:36:07 CDT)
- Re: Collective variable module Giacomo Fiorin (Thu Apr 10 2014 - 12:03:27 CDT)
  - Re: Collective variable module naresh kumar (Thu Apr 10 2014 - 12:54:02 CDT)
unsuscribe Cat Chenal (Thu Apr 10 2014 - 09:49:18 CDT)
MMPBSA Energy Calculations using VMD (Post-Processing) Aditya Ranganathan (Thu Apr 10 2014 - 08:25:41 CDT)
- Re: MMPBSA Energy Calculations using VMD (Post-Processing) Fotis Baltoumas (Thu Apr 10 2014 - 10:09:00 CDT)
  - Re: MMPBSA Energy Calculations using VMD (Post-Processing) James Starlight (Sat Apr 12 2014 - 01:53:35 CDT)
RE: slice of water box Hongbo Du (Wed Apr 09 2014 - 20:22:04 CDT)
- AW: slice of water box Norman Geist (Thu Apr 10 2014 - 01:46:05 CDT)
slice of water box Boshra Moradi (Wed Apr 09 2014 - 17:13:12 CDT)
Problems with energy minimization James Starlight (Wed Apr 09 2014 - 09:07:28 CDT)
- Re: Problems with energy minimization Subbarao Kanchi (Wed Apr 09 2014 - 09:14:55 CDT)
  - Re: Problems with energy minimization James Starlight (Wed Apr 09 2014 - 09:38:21 CDT)
AW: AW: Using nodelist file causes namd to hang Norman Geist (Wed Apr 09 2014 - 05:53:50 CDT)
- Re: AW: AW: Using nodelist file causes namd to hang Douglas Houston (Wed Apr 09 2014 - 06:16:35 CDT)
  - AW: AW: AW: Using nodelist file causes namd to hang Norman Geist (Wed Apr 09 2014 - 07:09:53 CDT)
- Re: AW: AW: Using nodelist file causes namd to hang Douglas Houston (Mon Jun 02 2014 - 04:50:40 CDT)
PMETolerance Natalie Esther Smith (Tue Apr 08 2014 - 23:07:52 CDT)
posting from Yahoo addresses disabled Jim Phillips (Tue Apr 08 2014 - 17:45:15 CDT)
Point group symmetry bmaiti_at_andrew.cmu.edu (Mon Apr 07 2014 - 18:20:08 CDT)
the dielectric constant use in pairwise interaction energy calculation of ligand and protein Patrick Chiu (Tue Apr 08 2014 - 08:45:11 CDT)
- RE: the dielectric constant use in pairwise interaction energy calculation of ligand and protein Hongbo Du (Tue Apr 08 2014 - 10:01:01 CDT)
Spinangle with refgroup : Warning: discontinuous rotation! nicolas martin (Mon Apr 07 2014 - 11:33:50 CDT)
- Re: Spinangle with refgroup : Warning: discontinuous rotation! nicolas martin (Wed Apr 09 2014 - 10:41:35 CDT)
Spinangle with refgroup : Warning: discontinuous rotation! nicolas martin (Mon Apr 07 2014 - 11:33:58 CDT)
Spinangle with refgroup : Warning: discontinuous rotation! nicolas martin (Mon Apr 07 2014 - 11:32:49 CDT)
- Re: Spinangle with refgroup : Warning: discontinuous rotation! Giacomo Fiorin (Mon Apr 07 2014 - 19:54:30 CDT)
  - Re: Spinangle with refgroup : Warning: discontinuous rotation! Giacomo Fiorin (Wed Apr 09 2014 - 11:18:13 CDT)
  - Re: Spinangle with refgroup : Warning: discontinuous rotation! nicolas martin (Thu Apr 10 2014 - 09:04:21 CDT)
Electronic density profile of lipid bilayer. Subbarao Kanchi (Sun Apr 06 2014 - 20:32:54 CDT)
Movie of a channel trajectory Javier Cáceres Delpiano (Sat Apr 05 2014 - 22:26:21 CDT)
- AW: Movie of a channel trajectory Norman Geist (Mon Apr 07 2014 - 02:05:25 CDT)
medwater config Hassan Kianinejad (Fri Apr 04 2014 - 19:15:32 CDT)
SHAKE or RATTLE algorithm Ramin Ekhteiari (Fri Apr 04 2014 - 15:08:04 CDT)
- Re: SHAKE or RATTLE algorithm Axel Kohlmeyer (Fri Apr 04 2014 - 15:44:45 CDT)
  - Re: SHAKE or RATTLE algorithm David Hardy (Fri Apr 04 2014 - 16:28:54 CDT)
Re: residue_rmsd.tcl segmentation fault Axel Kohlmeyer (Fri Apr 04 2014 - 03:03:55 CDT)
- AW: residue_rmsd.tcl segmentation fault Norman Geist (Fri Apr 04 2014 - 03:18:08 CDT)
- Re: residue_rmsd.tcl segmentation fault Axel Kohlmeyer (Fri Apr 04 2014 - 04:12:38 CDT)
residue_rmsd.tcl segmentation fault John Xi (Thu Apr 03 2014 - 21:49:05 CDT)
- AW: residue_rmsd.tcl segmentation fault Norman Geist (Fri Apr 04 2014 - 02:53:45 CDT)
  - Re: AW: residue_rmsd.tcl segmentation fault John Xi (Fri Apr 04 2014 - 07:04:45 CDT)
"Hands-on" Workshop on Computational Biophysics at Lake Tahoe, August 4-8, 2014 David Brandon (Thu Apr 03 2014 - 11:17:33 CDT)
Using position-dependent diffusion to simulate long colvars trajectories Ajasja LjubetiÄ (Thu Apr 03 2014 - 07:36:28 CDT)
6 equilibration steps at charmm gui server Ramin Ekhteiari (Thu Apr 03 2014 - 04:32:58 CDT)
- Re: 6 equilibration steps at charmm gui server Sunhwan Jo (Thu Apr 03 2014 - 09:34:23 CDT)
NAMD Pressure profile calculations Tao Qu (Wed Apr 02 2014 - 15:43:59 CDT)
Multiple dihedral with multiplicity of 7 greater than max of 6 Rawan Al Nsour (Wed Apr 02 2014 - 13:44:33 CDT)
Multiple dihedral with multiplicity of 7 greater than max of 6 Rawan Al Nsour (Wed Apr 02 2014 - 13:38:53 CDT)
- Re: Multiple dihedral with multiplicity of 7 greater than max of 6 Axel Kohlmeyer (Wed Apr 02 2014 - 13:52:18 CDT)
- Re: Multiple dihedral with multiplicity of 7 greater than max of 6 Kenno Vanommeslaeghe (Wed Apr 02 2014 - 14:05:49 CDT)
Excluding non bonded interactions between segments Fotis Baltoumas (Wed Apr 02 2014 - 07:40:29 CDT)
- Re: Excluding non bonded interactions between segments JÃ©rÃ´me HÃ©nin (Wed Apr 02 2014 - 08:09:21 CDT)
  - Re: Excluding non bonded interactions between segments Fotis Baltoumas (Tue Apr 08 2014 - 06:57:35 CDT)
    - Re: Excluding non bonded interactions between segments JÃ©rÃ´me HÃ©nin (Tue Apr 08 2014 - 06:56:22 CDT)
    - Re: Excluding non bonded interactions between segments Fotis Baltoumas (Tue Apr 08 2014 - 07:08:40 CDT)
Re: Assigning different temperatures to simulation Jhonatam Cordeiro Rodrigues (Wed Apr 02 2014 - 00:42:17 CDT)
- Re: Assigning different temperatures to simulation JÃ©rÃ´me HÃ©nin (Wed Apr 02 2014 - 02:35:40 CDT)
  - AW: Assigning different temperatures to simulation Norman Geist (Wed Apr 02 2014 - 02:45:57 CDT)
  - Re: Assigning different temperatures to simulation JÃ©rÃ´me HÃ©nin (Wed Apr 02 2014 - 03:16:30 CDT)
    - Re: Assigning different temperatures to simulation Jhonatam Cordeiro Rodrigues (Thu Apr 03 2014 - 15:24:09 CDT)
Random segfault for MPI based REMD at startup Norman Geist (Wed Apr 02 2014 - 00:34:20 CDT)
Assigning different temperatures to simulation Jhonatam Cordeiro Rodrigues (Tue Apr 01 2014 - 15:29:36 CDT)
- AW: Assigning different temperatures to simulation Norman Geist (Wed Apr 02 2014 - 00:02:58 CDT)
- AW: Assigning different temperatures to simulation Norman Geist (Wed Apr 02 2014 - 00:06:08 CDT)
question Eifler, Jay Q. (UMKC-Student) (Mon Mar 31 2014 - 11:47:16 CDT)
- Re: question JÃ©rÃ´me HÃ©nin (Mon Mar 31 2014 - 12:26:01 CDT)
accelerated MD log Felipe Merino (Mon Mar 31 2014 - 03:57:30 CDT)
Re: remd across gpus Francesco Pietra (Mon Mar 31 2014 - 02:41:24 CDT)
- AW: remd across gpus Norman Geist (Mon Mar 31 2014 - 04:13:21 CDT)
Constraint failure in RATTLE Francesco Pietra (Sun Mar 30 2014 - 02:31:54 CDT)
- Fwd: Constraint failure in RATTLE Francesco Pietra (Sun Mar 30 2014 - 03:07:50 CDT)
- Re: Constraint failure in RATTLE Massimiliano Porrini (Sun Mar 30 2014 - 06:49:34 CDT)
accelMD on GPUs Francesco Pietra (Sat Mar 29 2014 - 02:38:58 CDT)
remd across gpus Francesco Pietra (Sat Mar 29 2014 - 02:29:12 CDT)
- AW: remd across gpus Norman Geist (Mon Mar 31 2014 - 00:39:03 CDT)
Help to solve the error Flora Chettiar (Wed Mar 26 2014 - 04:00:46 CDT)
- Re: Help to solve the error Ivan Gregoretti (Wed Mar 26 2014 - 17:11:58 CDT)
  - Re: Help to solve the error Flora Chettiar (Thu Mar 27 2014 - 01:47:09 CDT)
    - Re: Help to solve the error Ivan Gregoretti (Thu Mar 27 2014 - 07:20:50 CDT)
hey! you! why did my simulation crash? Edward Lyman (Wed Mar 26 2014 - 10:42:46 CDT)
Question about accelerated MD Mare Libero (Tue Mar 25 2014 - 17:14:27 CDT)
- AW: Question about accelerated MD Norman Geist (Wed Mar 26 2014 - 02:34:20 CDT)
  - Re: AW: Question about accelerated MD Mare Libero (Wed Mar 26 2014 - 10:12:13 CDT)
Compiling with Open64 4.5.2.1 for AMD Opteron 6378 David Chin (Mon Mar 24 2014 - 10:44:54 CDT)
coarse-grained simulation: FATAL ERROR: UNABLE TO FIND BOND PARAMETERS FOR C5M P5 (ATOMS 1 2) Khaled Barakat (Sun Mar 23 2014 - 22:44:02 CDT)
PME: The Excluded Coulombic Interactions Hadi (Fri Mar 21 2014 - 22:56:50 CDT)
wrapping option in namd Research Jubilant (Wed Mar 19 2014 - 21:34:57 CDT)
- Re: wrapping option in namd Ivan Gregoretti (Wed Mar 19 2014 - 21:58:30 CDT)
  - Re: vmd-l: Re: wrapping option in namd Research Jubilant (Wed Mar 19 2014 - 22:38:16 CDT)
    - Re: vmd-l: Re: wrapping option in namd MEHRAN MB (Tue Apr 01 2014 - 21:44:36 CDT)
  - Fwd: vmd-l: Re: wrapping option in namd Christian Jorgensen (Mon Jun 23 2014 - 04:59:50 CDT)
Re: Restoring simulation from the previous run James Starlight (Wed Mar 19 2014 - 09:38:18 CDT)
Restoring simulation from the previous run James Starlight (Wed Mar 19 2014 - 03:32:31 CDT)
Improve scaling for large amount of fixed atoms Norman Geist (Wed Mar 19 2014 - 03:19:38 CDT)
- Re: Improve scaling for large amount of fixed atoms Tristan Croll (Wed Mar 19 2014 - 21:15:40 CDT)
changing damping coefficient during simulation Gozde Eskici (Tue Mar 18 2014 - 10:20:25 CDT)
iDataPlex Francesco Pietra (Mon Mar 17 2014 - 13:12:32 CDT)
- Re: iDataPlex Andrew Emerson (Tue Mar 18 2014 - 03:15:30 CDT)
  - Re: iDataPlex Francesco Pietra (Tue Mar 18 2014 - 04:03:29 CDT)
Detection of Internal water along MD trajectory James Starlight (Mon Mar 17 2014 - 04:14:38 CDT)
Free Energy Calculation Using Thermodynamic Integration Javad Noroozi (Mon Mar 17 2014 - 02:06:08 CDT)
TCL command "run" erratic Francesco Pietra (Sun Mar 16 2014 - 14:40:09 CDT)
- Fwd: TCL command "run" erratic Francesco Pietra (Sun Mar 16 2014 - 14:48:12 CDT)
  - Fwd: TCL command "run" erratic Francesco Pietra (Sun Mar 16 2014 - 14:57:53 CDT)
    - Re: Fwd: TCL command "run" erratic Aron Broom (Sun Mar 16 2014 - 15:58:34 CDT)
    - Re: Fwd: TCL command "run" erratic Francesco Pietra (Mon Mar 17 2014 - 02:22:26 CDT)
running benchmarks on NAMD-Lite Hassan Kianinejad (Fri Mar 14 2014 - 17:35:21 CDT)
Generalized Born Implicit solvation with implicit membrane Fotis Baltoumas (Fri Mar 14 2014 - 08:28:45 CDT)
- Re: Generalized Born Implicit solvation with implicit membrane Thomas Evangelidis (Fri Mar 14 2014 - 14:22:36 CDT)
Cross-correlation analysis in multidomain proteins James Starlight (Thu Mar 13 2014 - 05:32:22 CDT)
REï¼š REï¼š Re: REï¼š NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance sunyeping (Wed Mar 12 2014 - 09:42:34 CDT)
COLVAR related quesion Abir Ganguly (Tue Mar 11 2014 - 16:06:20 CDT)
- Re: COLVAR related quesion Giacomo Fiorin (Tue Mar 11 2014 - 16:19:24 CDT)
how to get cell vectors in tcl forces script Thomas Evangelidis (Tue Mar 11 2014 - 15:14:17 CDT)
- AW: how to get cell vectors in tcl forces script Norman Geist (Wed Mar 12 2014 - 02:29:43 CDT)
  - RE: how to get cell vectors in tcl forces script Cosseddu, Salvatore (Wed Mar 12 2014 - 07:05:43 CDT)
NAMD on Rescale Istvan Jonyer (Mon Mar 10 2014 - 20:22:10 CDT)
aa_ref-monomer-noh.dcd file in the tutorial of shape-based coarse grained (SBCG) simulation sunyeping (Mon Mar 10 2014 - 20:01:13 CDT)
Call for participation: ISQBP Meeting, Telluride 15-19.06.2014 Vlad Cojocaru (Mon Mar 10 2014 - 11:38:09 CDT)
aa_ref-monomer-noh.dcd in shape-based coarse grained simulation sunyeping (Sat Mar 08 2014 - 20:09:26 CST)
Accelerated Molecular Dynamics logs Johny Telecaster (Sat Mar 08 2014 - 09:37:05 CST)
Re: Accelerated MD in NAMD James Starlight (Sat Mar 08 2014 - 09:24:47 CST)
Regarding colvar distancez Subbarao Kanchi (Sat Mar 08 2014 - 05:00:28 CST)
- RE: Regarding colvar distancez Cosseddu, Salvatore (Sat Mar 08 2014 - 07:44:39 CST)
NAMD 2.9 quits early without error message. Ivan Gregoretti (Fri Mar 07 2014 - 11:36:17 CST)
- Re: NAMD 2.9 quits early without error message. Ivan Gregoretti (Fri Mar 07 2014 - 11:46:54 CST)
- RE: NAMD 2.9 quits early without error message. Morgan, Brittany (Fri Mar 07 2014 - 11:45:15 CST)
  - Re: NAMD 2.9 quits early without error message. Aron Broom (Fri Mar 07 2014 - 17:31:37 CST)
  - Re: NAMD 2.9 quits early without error message. Roy Fernando (Sat Mar 08 2014 - 10:03:21 CST)
    - Re: NAMD 2.9 quits early without error message. Ivan Gregoretti (Mon Mar 10 2014 - 18:45:17 CDT)
Monitoring progress of an ongoing molecular dynamics simulation Ivan Gregoretti (Fri Mar 07 2014 - 08:08:11 CST)
- RE: Monitoring progress of an ongoing molecular dynamics simulation Cosseddu, Salvatore (Fri Mar 07 2014 - 08:21:35 CST)
  - Re: Monitoring progress of an ongoing molecular dynamics simulation Ivan Gregoretti (Fri Mar 07 2014 - 08:52:43 CST)
- RE: Monitoring progress of an ongoing molecular dynamics simulation Bennion, Brian (Fri Mar 07 2014 - 11:44:01 CST)
force field parameter for graphene oxide Asis Jana (Fri Mar 07 2014 - 07:58:34 CST)
- Re: force field parameter for graphene oxide Kenno Vanommeslaeghe (Fri Mar 07 2014 - 11:28:50 CST)
AW: AW: benchmark info Norman Geist (Fri Mar 07 2014 - 01:40:25 CST)
compiling namd-lite Hassan Kianinejad (Thu Mar 06 2014 - 19:08:28 CST)
compiling namd-lite Hassan Kianinejad (Thu Mar 06 2014 - 18:55:54 CST)
How to maintain Density constant? Roy Fernando (Wed Mar 05 2014 - 15:43:59 CST)
- Re: How to maintain Density constant? Kenno Vanommeslaeghe (Wed Mar 05 2014 - 16:51:30 CST)
  - Re: How to maintain Density constant? Ivan Gregoretti (Thu Mar 06 2014 - 07:23:29 CST)
Restarting an FEP simulation Shyno Mathew (Wed Mar 05 2014 - 12:43:48 CST)
- Re: Restarting an FEP simulation Shyno Mathew (Mon Mar 10 2014 - 11:58:02 CDT)
  - Re: Restarting an FEP simulation Shyno Mathew (Sat Mar 22 2014 - 14:00:06 CDT)
VDW energy: positive or negative? PANAGIOTA KYRIAKOU (Tue Mar 04 2014 - 17:20:53 CST)
- Re: VDW energy: positive or negative? Axel Kohlmeyer (Tue Mar 04 2014 - 17:28:08 CST)
- Re: VDW energy: positive or negative? Kenno Vanommeslaeghe (Tue Mar 04 2014 - 17:50:50 CST)
  - Re: VDW energy: positive or negative? PANAGIOTA KYRIAKOU (Tue Mar 04 2014 - 18:24:54 CST)
How to stop omega trans-cis switching Alex Utev (CMP) (Mon Mar 03 2014 - 12:10:08 CST)
- How to stop omega trans-cis switching Alex Utev (CMP) (Mon Mar 03 2014 - 12:11:25 CST)
- Re: How to stop omega trans-cis switching Kenno Vanommeslaeghe (Mon Mar 03 2014 - 13:01:10 CST)
FEP result analysis Javad Noroozi (Sat Mar 01 2014 - 03:37:29 CST)
Generating .psf for amorphous disaccharide Maxwell Wesley Terban (Fri Feb 28 2014 - 13:10:56 CST)
- Re: Generating .psf for amorphous disaccharide JC Gumbart (Sat Mar 01 2014 - 21:41:45 CST)
Apply magnetic field through TCLBC Hongbo Du (Fri Feb 28 2014 - 11:22:04 CST)
- Re: Apply magnetic field through TCLBC Kenno Vanommeslaeghe (Mon Mar 03 2014 - 11:33:06 CST)
  - Re: Apply magnetic field through TCLBC Axel Kohlmeyer (Mon Mar 03 2014 - 11:46:25 CST)
  - RE: Apply magnetic field through TCLBC Hongbo Du (Mon Mar 03 2014 - 16:23:55 CST)
benchmark info Hassan Kianinejad (Thu Feb 27 2014 - 16:34:08 CST)
- AW: benchmark info Norman Geist (Fri Feb 28 2014 - 01:18:46 CST)
solvate plugin watsize value Sridhar Kumar Kannam (Wed Feb 26 2014 - 20:40:46 CST)
Persistent margin errors Vlastimil ZÃma (Wed Feb 26 2014 - 06:38:23 CST)
- Re: Persistent margin errors Vlastimil ZÃma (Wed Apr 16 2014 - 05:28:56 CDT)
  - AW: Re: Persistent margin errors Norman Geist (Wed Apr 16 2014 - 07:49:47 CDT)
Symmetry restraints break IMD handshaking Tristan Croll (Tue Feb 25 2014 - 21:23:26 CST)
ABF simulation fails with "FATAL ERROR: Low global exclusion count!" Maria Pikoula (Tue Feb 25 2014 - 11:02:24 CST)
- Re: ABF simulation fails with "FATAL ERROR: Low global exclusion count!" Giacomo Fiorin (Tue Feb 25 2014 - 20:19:28 CST)
  - Re: ABF simulation fails with "FATAL ERROR: Low global exclusion count!" Maria Pikoula (Fri Feb 28 2014 - 11:42:47 CST)
    - Re: ABF simulation fails with "FATAL ERROR: Low global exclusion count!" JÃ©rÃ´me HÃ©nin (Fri Feb 28 2014 - 11:58:59 CST)
    - Re: ABF simulation fails with "FATAL ERROR: Low global exclusion count!" Maria Pikoula (Fri Feb 28 2014 - 12:50:27 CST)
Free Energy Perturbation Javad Noroozi (Tue Feb 25 2014 - 00:36:30 CST)
- Re: Free Energy Perturbation JÃ©rÃ´me HÃ©nin (Thu Feb 27 2014 - 07:05:00 CST)
problem compiling NAMD Hassan Kianinejad (Mon Feb 24 2014 - 10:48:51 CST)
- Re: problem compiling NAMD David Hardy (Mon Feb 24 2014 - 13:18:32 CST)
  - Re: problem compiling NAMD David Hardy (Tue Feb 25 2014 - 12:39:11 CST)
    - Re: problem compiling NAMD Ivan Gregoretti (Tue Feb 25 2014 - 13:23:23 CST)
Re: Force Field Parameters for PEG Roy Fernando (Mon Feb 24 2014 - 10:22:47 CST)
- Re: Force Field Parameters for PEG Aron Broom (Mon Feb 24 2014 - 10:29:42 CST)
  - Re: Force Field Parameters for PEG Roy Fernando (Mon Feb 24 2014 - 10:48:08 CST)
    - Re: Force Field Parameters for PEG Axel Kohlmeyer (Mon Feb 24 2014 - 10:49:58 CST)
ç”å¤ï¼šREï¼š NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance sunyeping (Mon Feb 24 2014 - 03:37:02 CST)
- Re: ´ð¸´£ºRE£º NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance Axel Kohlmeyer (Mon Feb 24 2014 - 04:34:22 CST)
REï¼š Re: REï¼š NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance sunyeping (Mon Feb 24 2014 - 03:32:06 CST)
REï¼š NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance sunyeping (Sun Feb 23 2014 - 21:13:52 CST)
- Re: RE£º NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance Axel Kohlmeyer (Sun Feb 23 2014 - 21:26:40 CST)
NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance sunyeping (Sun Feb 23 2014 - 20:29:02 CST)
- Re: NAMDEnergy: FATAL ERROR: Please add +idlepoll to command line for proper performance Axel Kohlmeyer (Sun Feb 23 2014 - 20:57:18 CST)
Error when running MIC version of namd on Stampede Chen Wei (Fri Feb 21 2014 - 09:49:38 CST)
NAMD 2.9 Changing/Replacing atoms in multiple molecules Michal Skoczek (Fri Feb 21 2014 - 08:02:41 CST)
- Re: NAMD 2.9 Changing/Replacing atoms in multiple molecules Axel Kohlmeyer (Fri Feb 21 2014 - 08:11:33 CST)
  - Re: NAMD 2.9 Changing/Replacing atoms in multiple molecules Kenno Vanommeslaeghe (Fri Feb 21 2014 - 12:38:25 CST)
    - Re: NAMD 2.9 Changing/Replacing atoms in multiple molecules Tristan Croll (Fri Feb 21 2014 - 16:04:43 CST)
FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE zeynab mohamad hoseyni (Thu Feb 20 2014 - 13:31:50 CST)
runaway minimizations Bennion, Brian (Thu Feb 20 2014 - 12:06:54 CST)
About keep_water_out.tcl zeynab mohamad hoseyni (Thu Feb 20 2014 - 05:21:23 CST)
tools for Charmm Peter Reinke (Thu Feb 20 2014 - 02:39:59 CST)
- Re: tools for Charmm Kenno Vanommeslaeghe (Thu Feb 20 2014 - 10:16:40 CST)
  - Using nodelist file causes namd to hang Douglas Houston (Tue Apr 08 2014 - 04:29:34 CDT)
- Re: tools for Charmm Gianluca Interlandi (Thu Feb 20 2014 - 12:08:24 CST)
  - Re: tools for Charmm Kenno Vanommeslaeghe (Thu Feb 20 2014 - 13:05:13 CST)
Charmm Peter Reinke (Thu Feb 20 2014 - 02:31:35 CST)
- Re: Charmm Kenno Vanommeslaeghe (Thu Feb 20 2014 - 10:40:41 CST)
  - Re: Charmm Gianluca Interlandi (Thu Feb 20 2014 - 12:10:22 CST)
    - Re: Charmm Kenno Vanommeslaeghe (Thu Feb 20 2014 - 12:53:55 CST)
Re: Boyang Wang (Thu Feb 20 2014 - 00:53:46 CST)
- Re: Zhe Wu (Wed Oct 21 2015 - 14:16:02 CDT)
(no subject) Boyang Wang (Thu Feb 20 2014 - 00:05:03 CST)
- Re: write pdb bay__gulf618_at_sina.com (Thu Feb 20 2014 - 00:31:36 CST)
- AW: Norman Geist (Thu Feb 20 2014 - 00:41:55 CST)
Require Suggestion amit banerjee (Tue Feb 18 2014 - 23:39:40 CST)
- AW: Require Suggestion Norman Geist (Wed Feb 19 2014 - 01:42:09 CST)
pThr topology ÂÀÐ¡Ó¨ (Tue Feb 18 2014 - 21:05:27 CST)
protein-membrane interface hydration zeynab mohamad hoseyni (Tue Feb 18 2014 - 13:37:30 CST)
GPU/CPU workstation optimal simulation parameters for NAMD2.9 performance Pino, James Christopher (Tue Feb 18 2014 - 12:00:34 CST)
- AW: GPU/CPU workstation optimal simulation parameters for NAMD2.9 performance Norman Geist (Wed Feb 19 2014 - 01:38:53 CST)
Polarization effect of gold cluster Zhao Lina (Tue Feb 18 2014 - 06:20:20 CST)
- Re: Polarization effect of gold cluster Axel Kohlmeyer (Tue Feb 18 2014 - 06:32:07 CST)
  - Re: Polarization effect of gold cluster Zhao Lina (Fri Feb 21 2014 - 06:30:34 CST)
Failure of namd2.10 in keeping trace of cell in t-remd Francesco Pietra (Tue Feb 18 2014 - 05:44:34 CST)
- Fwd: Failure of namd2.10 in keeping trace of cell in t-remd Francesco Pietra (Tue Feb 18 2014 - 12:45:35 CST)
CHARMM36 and NAMD Douglas Houston (Tue Feb 18 2014 - 04:02:38 CST)
- Re: CHARMM36 and NAMD Kenno Vanommeslaeghe (Tue Feb 18 2014 - 20:23:37 CST)
REMD Boshra Moradi (Tue Feb 18 2014 - 02:08:53 CST)
- AW: REMD Norman Geist (Tue Feb 18 2014 - 02:59:07 CST)
ERROR: CALCULATED VDWA FORCE MAY NOT MATCH ENERGY! POSSIBLE BUG! Miss. State (Mon Feb 17 2014 - 17:05:09 CST)
- Re: ERROR: CALCULATED VDWA FORCE MAY NOT MATCH ENERGY! POSSIBLE BUG! Axel Kohlmeyer (Mon Feb 17 2014 - 17:26:41 CST)
  - Re: ERROR: CALCULATED VDWA FORCE MAY NOT MATCH ENERGY! POSSIBLE BUG! Axel Kohlmeyer (Mon Feb 17 2014 - 21:39:00 CST)
atomselect option for extracting protein-ligand complex KK R (Mon Feb 17 2014 - 16:16:43 CST)
- Re: atomselect option for extracting protein-ligand complex Axel Kohlmeyer (Mon Feb 17 2014 - 16:22:38 CST)
Membrane and NPAT José Villalaín (Mon Feb 17 2014 - 04:49:08 CST)
- Re: Membrane and NPAT Kenno Vanommeslaeghe (Mon Feb 17 2014 - 10:43:03 CST)
  - RE: Membrane and NPAT hannes.loeffler_at_stfc.ac.uk (Mon Feb 17 2014 - 10:53:49 CST)
Widom test particle insertion in NAMD Javad Noroozi (Mon Feb 17 2014 - 00:40:08 CST)
Guideline for selecting water box size. Hyuntae Na (Sun Feb 16 2014 - 18:49:00 CST)
- Re: Guideline for selecting water box size. Aron Broom (Sun Feb 16 2014 - 19:12:30 CST)
FAD topology and parameters Tanner, John J. (Sun Feb 16 2014 - 15:30:38 CST)
- Re: FAD topology and parameters flavio seixas (Mon Feb 17 2014 - 06:01:14 CST)
  - Re: FAD topology and parameters Tanner, John J. (Mon Feb 17 2014 - 10:15:52 CST)
    - Re: FAD topology and parameters Kenno Vanommeslaeghe (Tue Feb 18 2014 - 20:01:28 CST)
Instability in thermodynamic integration Maryam Sayadi (Sun Feb 16 2014 - 14:04:12 CST)
psf file does not contain cross-terms zeynab mohamad hoseyni (Sun Feb 16 2014 - 12:00:30 CST)
- Re: psf file does not contain cross-terms Axel Kohlmeyer (Sun Feb 16 2014 - 12:10:01 CST)
Adding hydrogen atoms to the crystall structure zeynab mohamad hoseyni (Sun Feb 16 2014 - 09:54:40 CST)
- Re: Adding hydrogen atoms to the crystall structure MEHRAN MB (Tue Feb 18 2014 - 10:10:53 CST)
  - Re: Adding hydrogen atoms to the crystall structure Thomas Evangelidis (Tue Feb 18 2014 - 10:44:56 CST)
  - Re: Adding hydrogen atoms to the crystall structure zeynab mohamad hoseyni (Tue Feb 18 2014 - 14:30:00 CST)
Non standar solvent Javad Noroozi (Sat Feb 15 2014 - 06:52:17 CST)
- Re: Non standar solvent MEHRAN MB (Tue Feb 18 2014 - 10:12:26 CST)
  - Re: Non standar solvent Roy Fernando (Tue Feb 18 2014 - 10:49:10 CST)
    - Re: Non standar solvent bdrakuli (Tue Feb 18 2014 - 11:43:58 CST)
Solvation in non standard solvent Javad Noroozi (Fri Feb 14 2014 - 05:58:59 CST)
Re: Job script for multi node job Subbarao Kanchi (Fri Feb 14 2014 - 05:22:55 CST)
- AW: Job script for multi node job Norman Geist (Fri Feb 14 2014 - 06:03:47 CST)
- Re: Job script for multi node job Subbarao Kanchi (Fri Feb 14 2014 - 08:24:13 CST)
Job script for multi node job Subbarao Kanchi (Fri Feb 14 2014 - 04:20:16 CST)
- AW: Job script for multi node job Norman Geist (Fri Feb 14 2014 - 05:12:56 CST)
- Re: Job script for multi node job Phil Greer (Fri Feb 14 2014 - 09:04:37 CST)
ABF force distribution Kasra Fattah (Thu Feb 13 2014 - 14:56:42 CST)
- Re: ABF force distribution MEHRAN MB (Tue Feb 18 2014 - 10:50:59 CST)
  - Re: ABF force distribution JÃ©rÃ´me HÃ©nin (Thu Feb 27 2014 - 06:59:48 CST)
    - Re: ABF force distribution Kasra Fattah (Sat Mar 01 2014 - 18:20:11 CST)
moving out of the box Ariel Talavera Perez (Thu Feb 13 2014 - 09:57:16 CST)
- Re: moving out of the box Ajasja LjubetiÄ (Thu Feb 13 2014 - 10:08:36 CST)
  - Re: moving out of the box Aaron Larsen (Thu Feb 13 2014 - 14:39:04 CST)
- AW: moving out of the box Norman Geist (Thu Feb 13 2014 - 14:21:26 CST)
  - Re: AW: moving out of the box Ariel Talavera Perez (Fri Feb 14 2014 - 08:38:01 CST)
- AW: moving out of the box Norman Geist (Thu Feb 13 2014 - 14:24:53 CST)
Dihedrals multiplicity! Anna Borlsky (Thu Feb 13 2014 - 09:24:46 CST)
- Re: Dihedrals multiplicity! Jeffrey Potoff (Thu Feb 13 2014 - 10:51:12 CST)
  - Re: Dihedrals multiplicity! Jeffrey Potoff (Thu Feb 13 2014 - 11:34:16 CST)
non-planarity problem! NOE restraints! Anna Borlsky (Thu Feb 13 2014 - 09:22:43 CST)
chloromethyl ketone patch? Jesper Madsen (Tue Feb 11 2014 - 16:49:21 CST)
Determining HIS protonation state using PropKa vmd plug-in zeynab mohamad hoseyni (Tue Feb 11 2014 - 06:30:09 CST)
Questions on calling external program to calculate force with NAMD Wasut Pornpatcharapong (Mon Feb 10 2014 - 15:41:48 CST)
Volume Entry Rawan Al Nsour (Mon Feb 10 2014 - 10:08:19 CST)
- Re: Volume Entry Axel Kohlmeyer (Mon Feb 10 2014 - 10:12:49 CST)
  - Re: Volume Entry Axel Kohlmeyer (Mon Feb 10 2014 - 10:45:37 CST)
PREMD in NAMD Matthew Ralph Adendorff (Mon Feb 10 2014 - 09:27:15 CST)
ABF simulations Abir Ganguly (Sat Feb 08 2014 - 15:38:01 CST)
- Re: ABF simulations Aron Broom (Mon Feb 10 2014 - 11:20:54 CST)
  - Re: ABF simulations Abir Ganguly (Thu Feb 13 2014 - 22:50:10 CST)
    - Re: ABF simulations Aron Broom (Fri Feb 14 2014 - 07:34:46 CST)
    - Re: ABF simulations MEHRAN MB (Tue Feb 18 2014 - 10:38:25 CST)
Log file is not being updated BATUHAN KAV (Mon Feb 10 2014 - 05:41:07 CST)
- Re: Log file is not being updated Ajasja LjubetiÄ (Mon Feb 10 2014 - 05:53:39 CST)
Strange glitches when performing energy minimization in MDFF simulations Tristan Croll (Sun Feb 09 2014 - 23:49:41 CST)
- RE: Strange glitches when performing energy minimization in MDFF simulations Tristan Croll (Mon Feb 10 2014 - 00:20:57 CST)
  - RE: Strange glitches when performing energy minimization in MDFF simulations Tristan Croll (Mon Feb 10 2014 - 18:24:37 CST)
Interactive molecular dynamics question Mare Libero (Sun Feb 09 2014 - 15:05:51 CST)
- Re: Interactive molecular dynamics question Chris Harrison (Sun Feb 09 2014 - 17:00:27 CST)
- Re: Interactive molecular dynamics question Axel Kohlmeyer (Sun Feb 09 2014 - 17:13:15 CST)
Specific Heat Calculation Rawan Al Nsour (Fri Feb 07 2014 - 20:56:14 CST)
Calculating density for a molecule Research Jubilant (Fri Feb 07 2014 - 11:36:41 CST)
- Re: Calculating density for a molecule Jeffrey Potoff (Fri Feb 07 2014 - 13:17:17 CST)
RSMDTT keyword for nucleic acids Aaron Larsen (Wed Feb 05 2014 - 14:43:13 CST)
PMEGridSizeX (number of grid points) is very small. Rawan Al Nsour (Wed Feb 05 2014 - 12:00:57 CST)
- RE: PMEGridSizeX (number of grid points) is very small. Bennion, Brian (Wed Feb 05 2014 - 12:28:37 CST)
  - Re: PMEGridSizeX (number of grid points) is very small. Maxim Belkin (Wed Feb 05 2014 - 12:44:35 CST)
    - Re: PMEGridSizeX (number of grid points) is very small. Aron Broom (Wed Feb 05 2014 - 15:10:53 CST)
Umbrella sampling using colvarconfig file with dihedrals Aaron Larsen (Wed Feb 05 2014 - 11:07:23 CST)
- Re: Umbrella sampling using colvarconfig file with dihedrals Giacomo Fiorin (Wed Feb 05 2014 - 11:25:36 CST)
- Re: Umbrella sampling using colvarconfig file with dihedrals Aron Broom (Wed Feb 05 2014 - 11:27:27 CST)
Question regarding loss of translational entropy calculation in FEP tutorial Monika Sharma (Tue Feb 04 2014 - 14:05:49 CST)
- Re: Question regarding loss of translational entropy calculation in FEP tutorial Aron Broom (Tue Feb 04 2014 - 14:22:31 CST)
- Re: Question regarding loss of translational entropy calculation in FEP tutorial Sunhwan Jo (Tue Feb 04 2014 - 14:47:17 CST)
ERROR: CALCULATED VDWA/B FORCES DOES NOT MATCH ENERGY Shalton Evans (Mon Feb 03 2014 - 21:13:41 CST)
Umbrella Sampling of Sugar Pseudorotation Aaron Larsen (Mon Feb 03 2014 - 13:32:45 CST)
- Re: Umbrella Sampling of Sugar Pseudorotation Dan F. X. Martingano (Mon Feb 03 2014 - 13:40:08 CST)
  - Re: Umbrella Sampling of Sugar Pseudorotation Aron Broom (Mon Feb 03 2014 - 15:01:34 CST)
    - Re: Umbrella Sampling of Sugar Pseudorotation Aaron Larsen (Mon Feb 03 2014 - 15:47:38 CST)
Hydration of protein-lipid interface zeynab mohamad hoseyni (Mon Feb 03 2014 - 10:27:20 CST)
problems about new molecule parameterization Tian Li (Thu Jan 30 2014 - 22:28:36 CST)
Structure size limitation in NAMD Nithyanan Annamalai (Wed Jan 29 2014 - 20:36:54 CST)
- Re: Structure size limitation in NAMD Axel Kohlmeyer (Wed Jan 29 2014 - 21:00:46 CST)
  - Re: Structure size limitation in NAMD Chris Harrison (Wed Jan 29 2014 - 23:41:09 CST)
ERROR: Molecule destroyed by fatal error Marlet Martinez (Mon Jan 27 2014 - 13:31:18 CST)
- Re: ERROR: Molecule destroyed by fatal error Axel Kohlmeyer (Mon Jan 27 2014 - 13:37:58 CST)
Steering colvars to defined points in space Tristan Croll (Sun Jan 26 2014 - 18:10:03 CST)
- Re: Steering colvars to defined points in space Aron Broom (Sun Jan 26 2014 - 19:23:56 CST)
  - RE: Steering colvars to defined points in space Tristan Croll (Sun Jan 26 2014 - 22:44:09 CST)
About Number of atoms in fixed atoms PDB doesn't match coordinate PDB Vidhya Sankar (Sat Jan 25 2014 - 21:01:01 CST)
- Re: About Number of atoms in fixed atoms PDB doesn't match coordinate PDB Sridhar Kumar Kannam (Sat Jan 25 2014 - 23:49:47 CST)
How to solvate a protein using C36 and not C27 zeynab mohamad hoseyni (Sat Jan 25 2014 - 11:08:14 CST)
PMF calculation crashes with constraint failure Magnus Andersson (Sat Jan 25 2014 - 11:02:11 CST)
- Re: PMF calculation crashes with constraint failure Giacomo Fiorin (Sun Jan 26 2014 - 15:37:10 CST)
How to solvate a protein using C36 and not C27 zeynab mohamad hoseyni (Sat Jan 25 2014 - 10:48:31 CST)
Liquid Simulation Failure Roy Fernando (Fri Jan 24 2014 - 18:54:44 CST)
AW: recent comparison of NAMD to other MD engines Norman Geist (Fri Jan 24 2014 - 13:22:51 CST)
recent comparison of NAMD to other MD engines Bennion, Brian (Wed Jan 22 2014 - 18:22:03 CST)
- Re: recent comparison of NAMD to other MD engines Giacomo Fiorin (Wed Jan 22 2014 - 20:38:29 CST)
  - AW: recent comparison of NAMD to other MD engines Norman Geist (Thu Jan 23 2014 - 01:32:54 CST)
  - Re: recent comparison of NAMD to other MD engines Hannes Loeffler (Thu Jan 23 2014 - 04:05:18 CST)
    - Re: recent comparison of NAMD to other MD engines JC Gumbart (Thu Jan 23 2014 - 11:14:22 CST)
    - AW: recent comparison of NAMD to other MD engines Norman Geist (Fri Jan 24 2014 - 01:01:04 CST)
- RE: recent comparison of NAMD to other MD engines Tristan Croll (Fri Jan 24 2014 - 02:44:05 CST)
  - RE: recent comparison of NAMD to other MD engines Bennion, Brian (Fri Jan 24 2014 - 12:59:21 CST)
- unsubscribe Zailo Leite (Fri Feb 14 2014 - 11:20:04 CST)
  - Re: unsubscribe MEHRAN MB (Fri Feb 14 2014 - 11:33:01 CST)
subscribe namd-l Ana Celia Vila Verde (Tue Jan 21 2014 - 11:22:15 CST)
Citating colvars module Salvatore Mario Cosseddu (Tue Jan 21 2014 - 11:20:50 CST)
- Re: Citating colvars module Giacomo Fiorin (Tue Jan 21 2014 - 11:12:55 CST)
Various questions Douglas Houston (Tue Jan 21 2014 - 09:42:14 CST)
- AW: Various questions Norman Geist (Wed Jan 22 2014 - 02:42:07 CST)
  - Re: AW: Various questions Douglas Houston (Wed Jan 22 2014 - 04:30:17 CST)
- Re: Various questions Douglas Houston (Wed Jan 22 2014 - 08:31:03 CST)
  - Re: Various questions Douglas Houston (Mon Feb 03 2014 - 03:52:42 CST)
    - AW: Re: Various questions Norman Geist (Mon Feb 03 2014 - 04:34:48 CST)
    - Re: AW: Re: Various questions Douglas Houston (Tue Feb 04 2014 - 07:26:05 CST)
Question regarding reverse CG to all-atom parikshit moitra (Tue Jan 21 2014 - 04:42:04 CST)
- AW: Question regarding reverse CG to all-atom Norman Geist (Tue Jan 21 2014 - 06:18:10 CST)
Reassure fluctuations in course of simulation James Starlight (Mon Jan 20 2014 - 03:19:51 CST)
Tct script for energy estimation James Starlight (Mon Jan 20 2014 - 03:16:23 CST)
Question regarding loss of translational entropy calculation in FEP tutorial Monika Sharma (Sun Jan 19 2014 - 11:32:02 CST)
About Psfgen error for Lipid molecules Vidhya Sankar (Sun Jan 19 2014 - 07:29:51 CST)
How to parametrize new atom types in Namd Dian Jiao (Fri Jan 17 2014 - 15:44:50 CST)
Re: namd-l digest V1 #1282 Istvan Jonyer (Fri Jan 17 2014 - 14:04:39 CST)
AW: keeping Crystal angles constant Norman Geist (Thu Jan 16 2014 - 02:36:51 CST)
keeping Crystal angles constant Mohan maruthi sena (Wed Jan 15 2014 - 12:03:58 CST)
- AW: keeping Crystal angles constant Norman Geist (Thu Jan 16 2014 - 02:13:08 CST)
RDF calculation with NAMD Dian Jiao (Tue Jan 14 2014 - 15:05:32 CST)
- Re: RDF calculation with NAMD Ana Celia Vila Verde (Tue Jan 21 2014 - 11:23:57 CST)
Re: Two GPU-based workstation James Starlight (Tue Jan 14 2014 - 04:45:38 CST)
- Re: Two GPU-based workstation Michael Purdy (Tue Jan 14 2014 - 08:05:40 CST)
  - Re: Two GPU-based workstation Johny Telecaster (Mon Mar 17 2014 - 02:38:56 CDT)
colvars with replica exchange molecular dynamics Francesco Pietra (Mon Jan 13 2014 - 14:29:41 CST)
- Re: colvars with replica exchange molecular dynamics Giacomo Fiorin (Mon Jan 13 2014 - 15:17:25 CST)
  - Re: colvars with replica exchange molecular dynamics Francesco Pietra (Tue Jan 14 2014 - 02:25:19 CST)
useGroupPressure Anna Borlsky (Fri Jan 10 2014 - 17:09:32 CST)
periodic boundary conditions Anna Borlsky (Fri Jan 10 2014 - 15:27:34 CST)
Thermodynamic integration questions Randall Hall (Thu Jan 09 2014 - 12:16:03 CST)
Difficulties with using the "rescalevels" command every MD timestep Spencer, Jacob (Thu Jan 09 2014 - 09:48:37 CST)
whidth value of orientation in colvars ¼¿ëÀÏ (Thu Jan 09 2014 - 02:27:59 CST)
- Re: whidth value of orientation in colvars Giacomo Fiorin (Thu Jan 09 2014 - 07:31:15 CST)
  - Re: whidth value of orientation in colvars ¼¿ëÀÏ (Thu Jan 09 2014 - 18:28:22 CST)
    - Re: whidth value of orientation in colvars Giacomo Fiorin (Fri Jan 10 2014 - 16:20:45 CST)
MD simulation Patch grid errors Jiann George Pazhamalil (Tue Jan 07 2014 - 17:33:06 CST)
- Re: MD simulation Patch grid errors Thomas Evangelidis (Tue Jan 07 2014 - 17:56:32 CST)
- Re: MD simulation Patch grid errors Jeffrey Potoff (Tue Jan 07 2014 - 18:03:29 CST)
  - Re: MD simulation Patch grid errors Jiann George Pazhamalil (Mon Jan 13 2014 - 21:37:41 CST)
    - Re: MD simulation Patch grid errors Jeffrey Potoff (Mon Jan 13 2014 - 22:34:42 CST)
    - Re: MD simulation Patch grid errors Thomas Evangelidis (Tue Jan 14 2014 - 02:19:55 CST)
Re: grcarma : a graphical user interface to carma Lenin DomÃnguez (Sun Jan 05 2014 - 18:20:50 CST)
CAN'T FIND DIHEDRAL PARAMETERS FOR CPH1 NR2 FE NPH Katherine Parra Pulido (Mon Jan 06 2014 - 23:33:49 CST)
- Re: CAN'T FIND DIHEDRAL PARAMETERS FOR CPH1 NR2 FE NPH Roy Fernando (Tue Jan 07 2014 - 08:05:22 CST)
citing SODIUM program Shyno Mathew (Sat Jan 04 2014 - 10:45:36 CST)
- Re: vmd-l: citing SODIUM program John Stone (Tue Jan 14 2014 - 09:19:27 CST)
About Warning in compilation of Namd Vidhya Sankar (Sat Jan 04 2014 - 03:41:57 CST)
- Re: About Warning in compilation of Namd Axel Kohlmeyer (Sat Jan 04 2014 - 06:21:55 CST)
question about force constant Lurong Pan (Fri Jan 03 2014 - 09:02:13 CST)
PBC only along the z axis. Sridhar Kumar Kannam (Thu Jan 02 2014 - 21:46:58 CST)
- Re: PBC only along the z axis. Subbarao Kanchi (Fri Jan 03 2014 - 00:18:53 CST)
  - Re: PBC only along the z axis. David Hardy (Fri Jan 03 2014 - 17:18:47 CST)
    - Re: PBC only along the z axis. Sridhar Kumar Kannam (Sat Jan 04 2014 - 18:25:28 CST)
Re: Temperature reassignment Thomas Evangelidis (Wed Jan 01 2014 - 09:27:57 CST)
- Re: Temperature reassignment PANAGIOTA KYRIAKOU (Wed Jan 01 2014 - 18:17:40 CST)
  - Re: Temperature reassignment Thomas Evangelidis (Thu Jan 02 2014 - 09:53:35 CST)
    - RE: Temperature reassignment Tristan Croll (Sun Jan 12 2014 - 21:32:03 CST)
About Tcl8.3 error in namd2.8 Vidhya Sankar (Wed Jan 01 2014 - 08:20:20 CST)
- Re: About Tcl8.3 error in namd2.8 Phil Miller (Wed Jan 01 2014 - 09:33:57 CST)
Fwd: Majordomo results Faezeh Mottaghitalab (Wed Jan 01 2014 - 05:19:11 CST)
- Re: Fwd: Majordomo results farzad kiani (Wed Jan 01 2014 - 14:57:29 CST)
  - Re: Fwd: Majordomo results Kuldeep Roy (Wed Jan 01 2014 - 16:33:22 CST)
error : segmentation fault Faezeh Mottaghitalab (Wed Jan 01 2014 - 05:18:30 CST)

Last message date: Tue Dec 29 2015 - 07:12:19 CST
Archived on: Thu Dec 31 2015 - 23:22:22 CST

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