Amber Archive May 2013 by thread
508 messages
:
Starting
Wed May 01 2013 - 05:00:02 PDT,
Ending
Fri May 31 2013 - 16:00:02 PDT
This period
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Re: [AMBER] improper Dihedral Specification
David A Case
(Wed May 01 2013 - 04:52:51 PDT)
Re: [AMBER] improper Dihedral Specification
Bill Ross
(Wed May 01 2013 - 15:51:21 PDT)
[AMBER] psf files from cellulose builder
Rasha Alqus
(Wed May 01 2013 - 08:59:05 PDT)
Re: [AMBER] DNA basestep stacking energy/interaction energy
BERGY
(Wed May 01 2013 - 14:56:34 PDT)
[AMBER] restart a md simulation
纪晓峰
(Wed May 01 2013 - 18:42:34 PDT)
[AMBER] restart a md simulation
纪晓峰
(Wed May 01 2013 - 18:53:03 PDT)
Re: [AMBER] restart a md simulation
Anselm Horn
(Thu May 02 2013 - 02:04:40 PDT)
[AMBER] occasional distortion of solute molecule
crazylyf
(Wed May 01 2013 - 21:23:15 PDT)
[AMBER] Amber 12 installation on GPU
Shozeb Haider
(Wed May 01 2013 - 23:51:46 PDT)
Re: [AMBER] Amber 12 installation on GPU
hannes.loeffler.stfc.ac.uk
(Thu May 02 2013 - 00:04:00 PDT)
Re: [AMBER] Amber 12 installation on GPU
David A Case
(Thu May 02 2013 - 06:29:48 PDT)
Re: [AMBER] Amber 12 installation on GPU
Ross Walker
(Thu May 02 2013 - 07:24:01 PDT)
[AMBER] cpptraj hbond: how to efficiently gather receptor-ligand hydrogen bonding statistics?
Jan-Philip Gehrcke
(Thu May 02 2013 - 05:30:36 PDT)
Re: [AMBER] cpptraj hbond: how to efficiently gather receptor-ligand hydrogen bonding statistics?
Daniel Roe
(Thu May 02 2013 - 07:22:02 PDT)
Re: [AMBER] cpptraj hbond: how to efficiently gather receptor-ligand hydrogen bonding statistics?
Jan-Philip Gehrcke
(Thu May 02 2013 - 08:02:56 PDT)
[AMBER] PM6 fails for DMSO system
me, Nancy
(Thu May 02 2013 - 14:48:59 PDT)
Re: [AMBER] PM6 fails for DMSO system
Jason Swails
(Thu May 02 2013 - 15:25:46 PDT)
Re: [AMBER] PM6 fails for DMSO system
me, Nancy
(Thu May 02 2013 - 16:34:05 PDT)
Re: [AMBER] PM6 fails for DMSO system
me, Nancy
(Fri May 03 2013 - 18:14:52 PDT)
Re: [AMBER] PM6 fails for DMSO system
Andreas Goetz
(Sat May 04 2013 - 18:43:36 PDT)
Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy
Jan-Philip Gehrcke
(Fri May 03 2013 - 02:53:36 PDT)
Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy
Jason Swails
(Fri May 03 2013 - 07:12:15 PDT)
Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy
Jan-Philip Gehrcke
(Fri May 03 2013 - 08:28:53 PDT)
[AMBER] vlimit exceed followed by SHAKE failure
seçkin Boz
(Fri May 03 2013 - 03:43:24 PDT)
Re: [AMBER] vlimit exceed followed by SHAKE failure
David A Case
(Fri May 03 2013 - 04:59:20 PDT)
Re: [AMBER] vlimit exceed followed by SHAKE failure
seçkin Boz
(Fri May 03 2013 - 05:47:52 PDT)
Re: [AMBER] vlimit exceed followed by SHAKE failure
David A Case
(Fri May 03 2013 - 11:59:33 PDT)
Re: [AMBER] vlimit exceed followed by SHAKE failure
seçkin Boz
(Tue May 07 2013 - 01:48:18 PDT)
Re: [AMBER] vlimit exceed followed by SHAKE failure
David A Case
(Tue May 07 2013 - 05:49:28 PDT)
Re: [AMBER] vlimit exceed followed by SHAKE failure
seçkin Boz
(Thu May 09 2013 - 04:06:22 PDT)
[AMBER] Advice on length of production simulation
Chris Chris
(Fri May 03 2013 - 09:01:49 PDT)
Re: [AMBER] Advice on length of production simulation
Marc van der Kamp
(Sat May 04 2013 - 04:08:34 PDT)
[AMBER] Need your help
Poornima Iyer
(Fri May 03 2013 - 10:43:22 PDT)
Re: [AMBER] Need your help
David A Case
(Fri May 03 2013 - 11:56:51 PDT)
[AMBER] MMPBSA Error: gb>0 is incompatible with periodic boundary conditions.
Angelica Parente
(Sat May 04 2013 - 02:08:02 PDT)
Re: [AMBER] MMPBSA Error: gb>0 is incompatible with periodic boundary conditions.
Jan-Philip Gehrcke
(Sat May 04 2013 - 08:59:59 PDT)
Re: [AMBER] MMPBSA Error: gb>0 is incompatible with periodic boundary conditions.
David A Case
(Sat May 04 2013 - 09:56:37 PDT)
Re: [AMBER] MMPBSA Error: gb>0 is incompatible with periodic boundary conditions.
Jason Swails
(Sat May 04 2013 - 17:06:02 PDT)
[AMBER] radial distribution function problem
Jio M
(Sat May 04 2013 - 02:35:28 PDT)
Re: [AMBER] radial distribution function problem
Daniel Roe
(Sat May 04 2013 - 09:10:52 PDT)
[AMBER] Ambertools13 installation issue
Chinthaka Ratnaweera
(Sat May 04 2013 - 13:21:17 PDT)
Re: [AMBER] Ambertools13 installation issue
Daniel Roe
(Sat May 04 2013 - 16:13:33 PDT)
Re: [AMBER] Ambertools13 installation issue
Chinthaka Ratnaweera
(Sat May 04 2013 - 17:16:20 PDT)
Re: [AMBER] Ambertools13 installation issue
Jason Swails
(Sat May 04 2013 - 20:07:59 PDT)
Re: [AMBER] Ambertools13 installation issue
Chinthaka Ratnaweera
(Sat May 04 2013 - 20:48:17 PDT)
Re: [AMBER] Ambertools13 installation issue
Jason Swails
(Sun May 05 2013 - 05:15:47 PDT)
Re: [AMBER] Ambertools13 installation issue
Chinthaka Ratnaweera
(Sun May 05 2013 - 06:46:40 PDT)
Re: [AMBER] Ambertools13 installation issue
Jason Swails
(Sun May 05 2013 - 08:26:44 PDT)
Re: [AMBER] Ambertools13 installation issue
Jason Swails
(Sat May 04 2013 - 17:14:46 PDT)
Re: [AMBER] Ambertools13 installation issue
Hector A. Baldoni
(Sat May 04 2013 - 17:25:14 PDT)
[AMBER] about halogen atom radius in MMPBSA calculation
Wang Bo
(Sat May 04 2013 - 21:05:00 PDT)
Re: [AMBER] about halogen atom radius in MMPBSA calculation
Nadine Homeyer
(Sun May 05 2013 - 23:00:16 PDT)
[AMBER] FW: Busco informacion sobre AMBER
Patricia Castro Gutierrez
(Sat May 04 2013 - 22:32:22 PDT)
Re: [AMBER] FW: Busco informacion sobre AMBER
ros
(Sat May 04 2013 - 23:09:29 PDT)
Re: [AMBER] FW: Busco informacion sobre AMBER
Sergio R Aragon
(Sat May 04 2013 - 23:11:18 PDT)
[AMBER] I can't visualize (in vmd) the output from an Accelerated MD (aMD) run
Jonathan Gough
(Sun May 05 2013 - 05:46:24 PDT)
Re: [AMBER] I can't visualize (in vmd) the output from an Accelerated MD (aMD) run
Daniel Roe
(Sun May 05 2013 - 09:05:58 PDT)
Re: [AMBER] I can't visualize (in vmd) the output from an Accelerated MD (aMD) run
Jonathan Gough
(Sun May 05 2013 - 09:20:37 PDT)
[AMBER] problem in cpptraj installation
Kshatresh Dutta Dubey
(Sun May 05 2013 - 07:56:57 PDT)
Re: [AMBER] problem in cpptraj installation
Daniel Roe
(Sun May 05 2013 - 08:59:03 PDT)
Re: [AMBER] problem in cpptraj installation
Kshatresh Dutta Dubey
(Sun May 05 2013 - 09:07:54 PDT)
Re: [AMBER] problem in cpptraj installation
Daniel Roe
(Sun May 05 2013 - 09:26:19 PDT)
Re: [AMBER] problem in cpptraj installation
Kshatresh Dutta Dubey
(Sun May 05 2013 - 10:58:09 PDT)
Re: [AMBER] problem in cpptraj installation
Daniel Roe
(Mon May 06 2013 - 07:54:20 PDT)
Re: [AMBER] problem in cpptraj installation
Kshatresh Dutta Dubey
(Mon May 06 2013 - 08:15:09 PDT)
Re: [AMBER] problem in cpptraj installation
Daniel Roe
(Mon May 06 2013 - 08:45:35 PDT)
[AMBER] Fwd:
Robin Jain
(Sun May 05 2013 - 22:33:23 PDT)
[AMBER] Bug in cpptraj (AmberTools 13)
Ake Sandgren
(Sun May 05 2013 - 23:07:12 PDT)
Re: [AMBER] Bug in cpptraj (AmberTools 13)
Daniel Roe
(Mon May 06 2013 - 07:15:12 PDT)
[AMBER] Ptraj_segmentation fault
KAMAKSHI SHARMA
(Mon May 06 2013 - 00:26:22 PDT)
Re: [AMBER] Ptraj_segmentation fault
Jason Swails
(Mon May 06 2013 - 05:36:30 PDT)
[AMBER] Protein-ligand docking
kanika sharma
(Mon May 06 2013 - 04:27:45 PDT)
Re: [AMBER] Protein-ligand docking
David A Case
(Mon May 06 2013 - 05:25:33 PDT)
[AMBER] Test for NTP, ntt=3
Deák Robert
(Mon May 06 2013 - 06:23:46 PDT)
Re: [AMBER] Test for NTP, ntt=3
Deák Robert
(Mon May 06 2013 - 06:25:38 PDT)
Re: [AMBER] Test for NTP, ntt=3
Jason Swails
(Mon May 06 2013 - 07:00:15 PDT)
Re: [AMBER] Test for NTP, ntt=3
Deák Robert
(Tue May 07 2013 - 02:47:41 PDT)
Re: [AMBER] Test for NTP, ntt=3
Deák Robert
(Tue May 07 2013 - 02:52:22 PDT)
Re: [AMBER] Test for NTP, ntt=3
Jason Swails
(Tue May 07 2013 - 05:54:27 PDT)
Re: [AMBER] Test for NTP, ntt=3
David A Case
(Tue May 07 2013 - 15:44:25 PDT)
[AMBER] MMPBSA.py error
Le,Huy Tuan
(Mon May 06 2013 - 06:39:25 PDT)
Re: [AMBER] MMPBSA.py error
Jason Swails
(Mon May 06 2013 - 06:50:45 PDT)
Re: [AMBER] MMPBSA.py error
Le,Huy Tuan
(Mon May 06 2013 - 07:10:54 PDT)
[AMBER] MMPBSA.py error
Kshatresh Dutta Dubey
(Mon May 06 2013 - 07:16:27 PDT)
Re: [AMBER] MMPBSA.py error
Chris Chris
(Mon May 06 2013 - 08:18:28 PDT)
Re: [AMBER] MMPBSA.py error
Kshatresh Dutta Dubey
(Mon May 06 2013 - 08:21:11 PDT)
Re: [AMBER] MMPBSA.py error
Jason Swails
(Mon May 06 2013 - 11:40:48 PDT)
Re: [AMBER] MMPBSA.py error
Kshatresh Dutta Dubey
(Mon May 06 2013 - 12:09:36 PDT)
Re: [AMBER] MMPBSA.py error
Jason Swails
(Mon May 06 2013 - 12:52:41 PDT)
Re: [AMBER] MMPBSA.py error
Kshatresh Dutta Dubey
(Mon May 06 2013 - 13:01:57 PDT)
Re: [AMBER] MMPBSA.py error
Jason Swails
(Mon May 06 2013 - 13:04:42 PDT)
[AMBER] mmpbsa error msg
Chinthaka Ratnaweera
(Mon May 06 2013 - 07:23:34 PDT)
Re: [AMBER] mmpbsa error msg
Chinthaka Ratnaweera
(Mon May 06 2013 - 07:26:05 PDT)
Re: [AMBER] mmpbsa error msg
Jason Swails
(Mon May 06 2013 - 11:41:57 PDT)
Re: [AMBER] mmpbsa error msg
Chinthaka Ratnaweera
(Mon May 06 2013 - 11:53:23 PDT)
Re: [AMBER] mmpbsa error msg
Jason Swails
(Mon May 06 2013 - 12:58:21 PDT)
[AMBER] the best APS is not zero, bonds involved by this atom are frozen
Ashutosh Shandilya
(Mon May 06 2013 - 08:15:43 PDT)
Re: [AMBER] the best APS is not zero, bonds involved by this atom are frozen
Ashutosh Shandilya
(Mon May 06 2013 - 08:24:40 PDT)
[AMBER] Open MPI failure
David Winogradoff
(Mon May 06 2013 - 09:18:43 PDT)
Re: [AMBER] Open MPI failure
Daniel Roe
(Mon May 06 2013 - 09:30:52 PDT)
Re: [AMBER] Open MPI failure
David Winogradoff
(Mon May 06 2013 - 10:25:29 PDT)
Re: [AMBER] Open MPI failure
Ross Walker
(Mon May 06 2013 - 10:30:03 PDT)
Re: [AMBER] Open MPI failure
David A Case
(Mon May 06 2013 - 12:49:25 PDT)
Re: [AMBER] Open MPI failure
David Winogradoff
(Tue May 07 2013 - 09:17:50 PDT)
Re: [AMBER] Open MPI failure
Daniel Roe
(Tue May 07 2013 - 10:38:44 PDT)
Re: [AMBER] Open MPI failure
David Winogradoff
(Tue May 07 2013 - 11:27:10 PDT)
Re: [AMBER] Open MPI failure
Daniel Roe
(Tue May 07 2013 - 13:41:46 PDT)
[AMBER] Leap adding salt No solvent overlap
Johannes Zuegg
(Mon May 06 2013 - 18:35:03 PDT)
Re: [AMBER] Leap adding salt No solvent overlap
Jason Swails
(Mon May 06 2013 - 20:19:25 PDT)
Re: [AMBER] Leap adding salt No solvent overlap
Daniel Roe
(Tue May 07 2013 - 07:52:01 PDT)
Re: [AMBER] Leap adding salt No solvent overlap
Johannes Zuegg
(Tue May 07 2013 - 16:51:44 PDT)
[AMBER] Atom does not have a type.
javier alejandro rendon carrillo
(Tue May 07 2013 - 00:48:42 PDT)
Re: [AMBER] Atom does not have a type.
David A Case
(Tue May 07 2013 - 05:32:22 PDT)
[AMBER] error while restart run
Subrata Paul
(Tue May 07 2013 - 04:22:41 PDT)
Re: [AMBER] error while restart run
David A Case
(Tue May 07 2013 - 05:45:21 PDT)
Re: [AMBER] error while restart run
Daniel Roe
(Tue May 07 2013 - 07:19:44 PDT)
[AMBER] problems solvating
Jonathan Gough
(Tue May 07 2013 - 05:58:05 PDT)
Re: [AMBER] problems solvating
Daniel Roe
(Tue May 07 2013 - 07:16:14 PDT)
[AMBER] Improper atom order
Reinis Danne
(Tue May 07 2013 - 05:26:53 PDT)
Re: [AMBER] Improper atom order
Karl N. Kirschner
(Wed May 08 2013 - 01:16:20 PDT)
Re: [AMBER] Improper atom order
Reinis Danne
(Wed May 08 2013 - 01:19:40 PDT)
Re: [AMBER] Improper atom order
Bill Ross
(Wed May 08 2013 - 17:34:52 PDT)
Re: [AMBER] Improper atom order
Reinis Danne
(Thu May 09 2013 - 00:21:05 PDT)
Re: [AMBER] Improper atom order
Bill Ross
(Sat May 11 2013 - 11:51:40 PDT)
[AMBER] PME and vdW cutoffs
George Tzotzos
(Tue May 07 2013 - 09:37:59 PDT)
Re: [AMBER] PME and vdW cutoffs
Andreas Goetz
(Tue May 07 2013 - 13:22:38 PDT)
[AMBER] Error in Membrane protein Simulation
Dipankar Roy
(Tue May 07 2013 - 09:39:40 PDT)
Re: [AMBER] Error in Membrane protein Simulation
David A Case
(Tue May 07 2013 - 15:44:54 PDT)
Re: [AMBER] Error in Membrane protein Simulation
Ross Walker
(Tue May 07 2013 - 16:42:53 PDT)
[AMBER] Optimal APBS parameters - Amber OR APBS defaults ?
Marek Maly
(Tue May 07 2013 - 11:27:06 PDT)
Re: [AMBER] Optimal APBS parameters - Amber OR APBS defaults ?
Ray Luo, Ph.D.
(Tue May 07 2013 - 14:52:26 PDT)
Re: [AMBER] Optimal APBS parameters - Amber OR APBS defaults ?
Marek Maly
(Tue May 07 2013 - 20:20:00 PDT)
[AMBER] when doing accelerated MD...
Jonathan Gough
(Tue May 07 2013 - 14:01:20 PDT)
Re: [AMBER] when doing accelerated MD...
Jesper Sørensen
(Tue May 07 2013 - 15:09:22 PDT)
Re: [AMBER] when doing accelerated MD...
Jonathan Gough
(Tue May 07 2013 - 15:16:57 PDT)
[AMBER] How to average rst ?
赵媛
(Tue May 07 2013 - 20:58:15 PDT)
Re: [AMBER] How to average rst ?
Daniel Roe
(Wed May 08 2013 - 08:02:01 PDT)
[AMBER] Kind of RESTYPE
setyanto md
(Tue May 07 2013 - 22:12:27 PDT)
Re: [AMBER] Kind of RESTYPE
David A Case
(Wed May 08 2013 - 05:14:32 PDT)
[AMBER] ATTN: need revision
seçkin Boz
(Wed May 08 2013 - 02:17:35 PDT)
Re: [AMBER] ATTN: need revision
Karl N. Kirschner
(Wed May 08 2013 - 03:00:03 PDT)
Re: [AMBER] ATTN: need revision
seçkin Boz
(Thu May 09 2013 - 04:45:46 PDT)
Re: [AMBER] ATTN: need revision
Karl N. Kirschner
(Mon May 13 2013 - 00:32:00 PDT)
Re: [AMBER] ATTN: need revision
Karl N. Kirschner
(Mon May 13 2013 - 04:07:44 PDT)
[AMBER] unstable sytem-help
Mary Varughese
(Wed May 08 2013 - 04:01:52 PDT)
[AMBER] Fwd: unstable sytem-help
Mary Varughese
(Thu May 09 2013 - 02:05:19 PDT)
Re: [AMBER] Fwd: unstable sytem-help
David A Case
(Thu May 09 2013 - 06:03:28 PDT)
Re: [AMBER] Fwd: unstable sytem-help
Mary Varughese
(Thu May 09 2013 - 06:50:32 PDT)
Re: [AMBER] Fwd: unstable sytem-help
David A Case
(Fri May 10 2013 - 03:48:11 PDT)
Re: [AMBER] Fwd: unstable sytem-help
Mary Varughese
(Fri May 10 2013 - 16:44:16 PDT)
[AMBER] Assistance required for MCPB program
BALA SUBRAMANI G L
(Wed May 08 2013 - 05:19:51 PDT)
[AMBER] fw: hey
Wholly Peach
(Wed May 08 2013 - 06:32:28 PDT)
[AMBER] normal modes and intensity for raman spectrum
Rasha Alqus
(Wed May 08 2013 - 08:51:56 PDT)
Re: [AMBER] normal modes and intensity for raman spectrum
Adrian Roitberg
(Wed May 08 2013 - 10:54:46 PDT)
[AMBER] pmemd performance on AMD 16cores x 4 (total 64 CPU cores) + 1 GPU
sun
(Wed May 08 2013 - 09:40:23 PDT)
Re: [AMBER] pmemd performance on AMD 16cores x 4 (total 64 CPU cores) + 1 GPU
Sergio R Aragon
(Wed May 08 2013 - 12:19:20 PDT)
Re: [AMBER] pmemd performance on AMD 16cores x 4 (total 64 CPU cores) + 1 GPU
Scott Le Grand
(Wed May 08 2013 - 12:51:30 PDT)
Re: [AMBER] pmemd performance on AMD 16cores x 4 (total 64 CPU cores) + 1 GPU
Ross Walker
(Wed May 08 2013 - 13:15:31 PDT)
[AMBER] error running pmemd cuda tests
Blake Mertz
(Wed May 08 2013 - 11:32:46 PDT)
Re: [AMBER] error running pmemd cuda tests
Jason Swails
(Wed May 08 2013 - 12:19:55 PDT)
Re: [AMBER] error running pmemd cuda tests
Blake Mertz
(Wed May 08 2013 - 18:53:53 PDT)
Re: [AMBER] error running pmemd cuda tests
ET
(Thu May 09 2013 - 00:57:17 PDT)
Re: [AMBER] error running pmemd cuda tests
Blake Mertz
(Thu May 09 2013 - 06:15:57 PDT)
Re: [AMBER] error running pmemd cuda tests
Jason Swails
(Thu May 09 2013 - 07:28:54 PDT)
Re: [AMBER] error running pmemd cuda tests
ET
(Fri May 10 2013 - 09:33:19 PDT)
Re: [AMBER] Paper detailing GPU Simulations Compared to CPU code
ET
(Wed May 08 2013 - 17:12:19 PDT)
[AMBER] About free energy decomposition
赵媛
(Wed May 08 2013 - 20:23:32 PDT)
Re: [AMBER] About free energy decomposition
Bill Miller III
(Fri May 10 2013 - 21:02:10 PDT)
[AMBER] DNA ligand system broke up- help please
Mary Varughese
(Thu May 09 2013 - 03:45:09 PDT)
[AMBER] AMBER GPU Cooling/usage Question
ET
(Thu May 09 2013 - 05:44:08 PDT)
Re: [AMBER] AMBER GPU Cooling/usage Question
Ross Walker
(Thu May 09 2013 - 06:27:54 PDT)
Re: [AMBER] AMBER GPU Cooling/usage Question
ET
(Fri May 10 2013 - 08:49:23 PDT)
[AMBER] how to create parameter file for Zn
BALA SUBRAMANI G L
(Thu May 09 2013 - 06:13:16 PDT)
[AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure
Andre C. Stiel
(Thu May 09 2013 - 10:02:48 PDT)
Re: [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure
Daniel Roe
(Thu May 09 2013 - 12:41:08 PDT)
Re: [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure
Andre C. Stiel
(Fri May 10 2013 - 05:03:18 PDT)
Re: [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure
Andre C. Stiel
(Fri May 10 2013 - 05:31:38 PDT)
Re: [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure
Daniel Roe
(Fri May 10 2013 - 05:40:01 PDT)
Re: [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure
Andre C. Stiel
(Fri May 10 2013 - 05:41:21 PDT)
Re: [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure
Daniel Roe
(Fri May 10 2013 - 05:57:11 PDT)
[AMBER] Convergence criterion
Anselm Horn
(Fri May 17 2013 - 12:46:16 PDT)
Re: [AMBER] Convergence criterion
David A Case
(Fri May 17 2013 - 17:21:40 PDT)
Re: [AMBER] Convergence criterion
Anselm Horn
(Sat May 18 2013 - 04:14:13 PDT)
Re: [AMBER] Convergence criterion
Andreas Goetz
(Sat May 18 2013 - 13:00:28 PDT)
Re: [AMBER] Convergence criterion
Anselm Horn
(Sat May 18 2013 - 18:06:07 PDT)
[AMBER] Glass Transition Temperature
Hector A. Baldoni
(Thu May 09 2013 - 12:18:39 PDT)
Re: [AMBER] Glass Transition Temperature
David A Case
(Fri May 10 2013 - 08:42:23 PDT)
[AMBER] apbsgrid error during sander.APBS calculation
Marek Maly
(Thu May 09 2013 - 17:18:54 PDT)
Re: [AMBER] apbsgrid error during sander.APBS calculation
Robert Konecny
(Thu May 09 2013 - 18:53:16 PDT)
Re: [AMBER] apbsgrid error during sander.APBS calculation
Marek Maly
(Fri May 10 2013 - 04:48:06 PDT)
[AMBER] Problem with the SMD aplication to proton transfer
Santi Tolosa
(Fri May 10 2013 - 04:05:56 PDT)
Re: [AMBER] Problem with the SMD aplication to proton transfer
Brian Radak
(Fri May 10 2013 - 05:55:58 PDT)
[AMBER] drmsd
Chris Chris
(Fri May 10 2013 - 22:23:22 PDT)
Re: [AMBER] drmsd
Daniel Roe
(Sat May 11 2013 - 08:17:38 PDT)
[AMBER] NaN from Mg2+ near ASP while running aMD
Jonathan Gough
(Sun May 12 2013 - 12:34:31 PDT)
Re: [AMBER] NaN from Mg2+ near ASP while running aMD
Jonathan Gough
(Sun May 12 2013 - 12:38:51 PDT)
[AMBER] sander.MPI is extremely slow
Kshatresh Dutta Dubey
(Sun May 12 2013 - 21:48:15 PDT)
Re: [AMBER] sander.MPI is extremely slow
Ross Walker
(Mon May 13 2013 - 03:23:14 PDT)
[AMBER] MMPBSA.py
Urszula Uciechowska
(Sun May 12 2013 - 23:24:35 PDT)
Re: [AMBER] MMPBSA.py
Jason Swails
(Mon May 13 2013 - 05:03:38 PDT)
[AMBER] The force constants of bond and angle items are zero when the MCPB program reads the internal force constant matrix
JiYuan Liu
(Mon May 13 2013 - 00:43:43 PDT)
[AMBER] Regarding mmpbsa.py
dilrajl.bii.a-star.edu.sg
(Mon May 13 2013 - 03:55:57 PDT)
Re: [AMBER] Regarding mmpbsa.py
David A Case
(Mon May 13 2013 - 04:54:25 PDT)
Re: [AMBER] Regarding mmpbsa.py
Jason Swails
(Mon May 13 2013 - 05:00:28 PDT)
[AMBER] rmsd vs rmsf
nguyentb.bii.a-star.edu.sg
(Tue May 21 2013 - 02:36:08 PDT)
Re: [AMBER] rmsd vs rmsf
Carlos Simmerling
(Tue May 21 2013 - 04:17:08 PDT)
Re: [AMBER] rmsd vs rmsf
Jason Swails
(Tue May 21 2013 - 04:36:55 PDT)
Re: [AMBER] rmsd vs rmsf
nguyentb.bii.a-star.edu.sg
(Tue May 21 2013 - 05:30:08 PDT)
[AMBER] pairwise decomposition using mmpbsa.py
dilrajl.bii.a-star.edu.sg
(Wed May 22 2013 - 05:34:45 PDT)
Re: [AMBER] pairwise decomposition using mmpbsa.py
Jason Swails
(Wed May 22 2013 - 05:52:38 PDT)
[AMBER] RMSD calculation between trajectories
dilrajl.bii.a-star.edu.sg
(Tue May 28 2013 - 05:42:42 PDT)
Re: [AMBER] RMSD calculation between trajectories
Niel Henriksen
(Tue May 28 2013 - 05:59:50 PDT)
Re: [AMBER] RMSD calculation between trajectories
Niel Henriksen
(Tue May 28 2013 - 06:13:30 PDT)
Re: [AMBER] RMSD calculation between trajectories
Daniel Roe
(Tue May 28 2013 - 07:24:01 PDT)
Re: [AMBER] RMSD calculation between trajectories
dilrajl.bii.a-star.edu.sg
(Wed May 29 2013 - 05:10:58 PDT)
Re: [AMBER] RMSD calculation between trajectories
Daniel Roe
(Wed May 29 2013 - 07:11:18 PDT)
Re: [AMBER] RMSD calculation between trajectories
dilrajl.bii.a-star.edu.sg
(Thu May 30 2013 - 05:27:31 PDT)
Re: [AMBER] RMSD calculation between trajectories
Daniel Roe
(Thu May 30 2013 - 05:56:56 PDT)
[AMBER] Assistance required for capActivesite program
Bala Subramani
(Mon May 13 2013 - 06:09:05 PDT)
[AMBER] Inconsistent results for TI calculations
Thomas Exner
(Mon May 13 2013 - 07:47:36 PDT)
Re: [AMBER] Inconsistent results for TI calculations
steinbrt.rci.rutgers.edu
(Mon May 13 2013 - 09:31:50 PDT)
Re: [AMBER] Inconsistent results for TI calculations
Antonios Kolocouris
(Mon May 13 2013 - 09:48:58 PDT)
[AMBER] (nessun oggetto)
Maurizio CELENTANO
(Mon May 13 2013 - 07:52:58 PDT)
Re: [AMBER] (nessun oggetto)
David A Case
(Mon May 13 2013 - 09:08:29 PDT)
Re: [AMBER] (nessun oggetto)
Maurizio CELENTANO
(Mon May 13 2013 - 11:00:31 PDT)
Re: [AMBER] (nessun oggetto)
David A Case
(Mon May 13 2013 - 13:08:58 PDT)
[AMBER] cpptraj strange warning with cluster command
Miguel Ortiz Lombardía
(Mon May 13 2013 - 08:26:03 PDT)
Re: [AMBER] cpptraj strange warning with cluster command
Daniel Roe
(Mon May 13 2013 - 08:35:59 PDT)
Re: [AMBER] cpptraj strange warning with cluster command
Miguel Ortiz Lombardía
(Mon May 13 2013 - 09:08:40 PDT)
[AMBER] mpi4py installation error
Kshatresh Dutta Dubey
(Mon May 13 2013 - 11:18:50 PDT)
Re: [AMBER] mpi4py installation error
Daniel Roe
(Mon May 13 2013 - 12:15:39 PDT)
Re: [AMBER] mpi4py installation error
Kshatresh Dutta Dubey
(Mon May 13 2013 - 12:24:21 PDT)
[AMBER] amber tutorial A15
yanyuna
(Mon May 13 2013 - 18:16:19 PDT)
Re: [AMBER] amber tutorial A15
David A Case
(Mon May 13 2013 - 18:59:00 PDT)
Re: [AMBER] amber tutorial A15
yanyuna
(Mon May 13 2013 - 19:04:04 PDT)
Re: [AMBER] amber tutorial A15
David A Case
(Tue May 14 2013 - 03:35:12 PDT)
Re: [AMBER] amber tutorial A15
yanyuna
(Mon May 13 2013 - 19:30:21 PDT)
[AMBER] assistance required for MTK++
BALA SUBRAMANI G L
(Tue May 14 2013 - 00:20:27 PDT)
[AMBER] error while using tleap with protein more than 248 residues
sandeep singh
(Sun May 12 2013 - 22:05:11 PDT)
Re: [AMBER] error while using tleap with protein more than 248 residues
David A Case
(Tue May 14 2013 - 03:32:20 PDT)
Re: [AMBER] error while using tleap with protein more than 248 residues
Daniel Roe
(Tue May 14 2013 - 07:48:39 PDT)
[AMBER] Random Acceleration Molecular Dynamics (RAMD)
Lars Skjærven
(Tue May 14 2013 - 03:16:50 PDT)
Re: [AMBER] Random Acceleration Molecular Dynamics (RAMD)
Vlad Cojocaru
(Tue May 14 2013 - 03:55:48 PDT)
[AMBER] Nonpolar contribution in MMPBSA is very large
Kshatresh Dutta Dubey
(Tue May 14 2013 - 03:34:19 PDT)
Re: [AMBER] Nonpolar contribution in MMPBSA is very large
Jason Swails
(Tue May 14 2013 - 05:04:22 PDT)
Re: [AMBER] Nonpolar contribution in MMPBSA is very large
Kshatresh Dutta Dubey
(Tue May 14 2013 - 05:32:33 PDT)
Re: [AMBER] Nonpolar contribution in MMPBSA is very large
Jan-Philip Gehrcke
(Tue May 14 2013 - 05:39:16 PDT)
Re: [AMBER] Nonpolar contribution in MMPBSA is very large
Kshatresh Dutta Dubey
(Tue May 14 2013 - 05:48:14 PDT)
Re: [AMBER] Nonpolar contribution in MMPBSA is very large
Jason Swails
(Tue May 14 2013 - 07:21:02 PDT)
Re: [AMBER] Nonpolar contribution in MMPBSA is very large
Kshatresh Dutta Dubey
(Tue May 14 2013 - 07:38:19 PDT)
[AMBER] Assistance required for capActivesite program
BALA SUBRAMANI G L
(Mon May 13 2013 - 06:08:23 PDT)
Re: [AMBER] Assistance required for capActivesite program
steinbrt.rci.rutgers.edu
(Tue May 14 2013 - 04:54:03 PDT)
[AMBER] random seed not in output file -> run not reproducible
Jan-Philip Gehrcke
(Tue May 14 2013 - 04:02:30 PDT)
Re: [AMBER] random seed not in output file -> run not reproducible
Ross Walker
(Tue May 14 2013 - 04:35:08 PDT)
Re: [AMBER] random seed not in output file -> run not reproducible
Jason Swails
(Tue May 14 2013 - 05:02:20 PDT)
Re: [AMBER] random seed not in output file -> run not reproducible
Ross Walker
(Tue May 14 2013 - 05:04:20 PDT)
Re: [AMBER] random seed not in output file -> run not reproducible
Jason Swails
(Tue May 14 2013 - 05:20:43 PDT)
Re: [AMBER] random seed not in output file -> run not reproducible
Jan-Philip Gehrcke
(Tue May 14 2013 - 05:15:51 PDT)
[AMBER] Free Energy for the G Quadruplex DNA including channel potassium ions
Debayan Chakraborty
(Tue May 14 2013 - 05:03:26 PDT)
[AMBER] assistance required for bcl scripts
BALA SUBRAMANI G L
(Tue May 14 2013 - 05:24:41 PDT)
[AMBER] SMD for proton transfer
Santi Tolosa
(Tue May 14 2013 - 06:19:54 PDT)
Re: [AMBER] SMD for proton transfer
M. L. Dodson
(Tue May 14 2013 - 06:47:30 PDT)
[AMBER] Problem with cpptraj vs ptraj
imarcos
(Tue May 14 2013 - 06:33:50 PDT)
Re: [AMBER] Problem with cpptraj vs ptraj
Daniel Roe
(Tue May 14 2013 - 07:12:12 PDT)
Re: [AMBER] Problem with cpptraj vs ptraj
imarcos
(Thu May 16 2013 - 03:55:15 PDT)
[AMBER] preferred nucleic acids pbsa model
Le,Huy Tuan
(Tue May 14 2013 - 06:55:40 PDT)
[AMBER] memory failure
Jonathan Gough
(Tue May 14 2013 - 10:39:27 PDT)
Re: [AMBER] memory failure
Jonathan Gough
(Tue May 14 2013 - 10:41:56 PDT)
Re: [AMBER] memory failure
David A Case
(Tue May 14 2013 - 11:15:08 PDT)
Re: [AMBER] memory failure
Jonathan Gough
(Tue May 14 2013 - 12:45:05 PDT)
[AMBER] assistance required for prep & frcmod file preparation
BALA SUBRAMANI G L
(Wed May 15 2013 - 00:00:24 PDT)
[AMBER] NAMD TO AMBER
Rasha Alqus
(Wed May 15 2013 - 03:37:32 PDT)
[AMBER] pmemd.CUDA installation problem
Cenk \(Jenk\) Andac
(Wed May 15 2013 - 09:38:14 PDT)
Re: [AMBER] pmemd.CUDA installation problem
Jason Swails
(Wed May 15 2013 - 10:03:29 PDT)
Re: [AMBER] pmemd.CUDA installation problem
Cenk \(Jenk\) Andac
(Wed May 15 2013 - 23:11:12 PDT)
Re: [AMBER] pmemd.CUDA installation problem
Cenk \(Jenk\) Andac
(Thu May 16 2013 - 00:24:56 PDT)
[AMBER] Interpreting .prmtop files
David Winogradoff
(Wed May 15 2013 - 14:13:54 PDT)
Re: [AMBER] Interpreting .prmtop files
Hai Nguyen
(Wed May 15 2013 - 14:18:33 PDT)
Re: [AMBER] Interpreting .prmtop files
Jason Swails
(Wed May 15 2013 - 16:18:14 PDT)
Re: [AMBER] Interpreting .prmtop files
David Winogradoff
(Thu May 16 2013 - 06:07:14 PDT)
Re: [AMBER] Interpreting .prmtop files
David Winogradoff
(Thu May 16 2013 - 08:49:12 PDT)
Re: [AMBER] Interpreting .prmtop files
Jason Swails
(Thu May 16 2013 - 09:15:16 PDT)
Re: [AMBER] Interpreting .prmtop files
David Winogradoff
(Tue May 28 2013 - 08:45:27 PDT)
[AMBER] SMD pulling GPU
José Guilherme Vilhena Albuquerque d'Orey
(Thu May 16 2013 - 01:44:07 PDT)
Re: [AMBER] SMD pulling GPU
James Murdock
(Thu May 16 2013 - 03:42:30 PDT)
Re: [AMBER] SMD pulling GPU
Ross Walker
(Thu May 16 2013 - 07:58:09 PDT)
Re: [AMBER] SMD pulling GPU
José Guilherme Vilhena Albuquerque d'Orey
(Thu May 16 2013 - 08:29:39 PDT)
Re: [AMBER] SMD pulling GPU
Ross Walker
(Thu May 16 2013 - 09:59:41 PDT)
[AMBER] References abou FF12SB
Alan
(Thu May 16 2013 - 05:35:56 PDT)
[AMBER] cluster
Mannan
(Tue May 21 2013 - 03:48:43 PDT)
Re: [AMBER] cluster
Daniel Roe
(Tue May 21 2013 - 07:28:47 PDT)
Re: [AMBER] References abou FF12SB
Carlos Simmerling
(Tue May 21 2013 - 04:52:44 PDT)
[AMBER] ff10 from amber11 maybe not using OL3??
Amparo Garcia Lopez
(Thu May 16 2013 - 09:31:16 PDT)
Re: [AMBER] ff10 from amber11 maybe not using OL3??
Niel Henriksen
(Thu May 16 2013 - 11:57:32 PDT)
Re: [AMBER] ff10 from amber11 maybe not using OL3??
pavel.banas.upol.cz
(Thu May 16 2013 - 13:16:00 PDT)
Re: [AMBER] ff10 from amber11 maybe not using OL3??
Amparo Garcia Lopez
(Thu May 16 2013 - 14:16:09 PDT)
Re: [AMBER] ff10 from amber11 maybe not using OL3??
Amparo Garcia Lopez
(Thu May 16 2013 - 14:44:00 PDT)
Re: [AMBER] ff10 from amber11 maybe not using OL3??
Ilyas Yildirim
(Thu May 16 2013 - 15:18:31 PDT)
Re: [AMBER] ff10 from amber11 maybe not using OL3??
pavel.banas.upol.cz
(Thu May 16 2013 - 16:05:04 PDT)
Re: [AMBER] ff10 from amber11 maybe not using OL3??
Amparo Garcia Lopez
(Fri May 17 2013 - 00:58:45 PDT)
Re: [AMBER] ff10 from amber11 maybe not using OL3??
David A Case
(Fri May 17 2013 - 05:35:07 PDT)
[AMBER] How to dump distance information in the form of a vector file?
Sajeewa Pemasinghe
(Thu May 16 2013 - 14:19:53 PDT)
Re: [AMBER] How to dump distance information in the form of a vector file?
Daniel Roe
(Thu May 16 2013 - 14:53:19 PDT)
Re: [AMBER] How to dump distance information in the form of a vector file?
Sajeewa Pemasinghe
(Thu May 16 2013 - 15:38:27 PDT)
Re: [AMBER] How to dump distance information in the form of a vector file?
Daniel Roe
(Thu May 16 2013 - 15:48:18 PDT)
[AMBER] Parameters for Aluminum Ion
Sun
(Thu May 16 2013 - 21:00:48 PDT)
[AMBER] How to specify a vector to keep track of the velocities of all residues during a simulation?
Sajeewa Pemasinghe
(Fri May 17 2013 - 10:05:13 PDT)
Re: [AMBER] How to specify a vector to keep track of the velocities of all residues during a simulation?
Daniel Roe
(Fri May 17 2013 - 10:34:40 PDT)
Re: [AMBER] How to specify a vector to keep track of the velocities of all residues during a simulation?
Sajeewa Pemasinghe
(Fri May 17 2013 - 10:58:14 PDT)
Re: [AMBER] How to specify a vector to keep track of the velocities of all residues during a simulation?
David A Case
(Fri May 17 2013 - 11:11:51 PDT)
[AMBER] force field parameters for acetylated lysine
Senthil Natesan
(Fri May 17 2013 - 11:03:52 PDT)
Re: [AMBER] force field parameters for acetylated lysine
Karl N. Kirschner
(Tue May 21 2013 - 00:17:27 PDT)
Re: [AMBER] force field parameters for acetylated lysine
Senthil Natesan
(Tue May 21 2013 - 06:28:15 PDT)
[AMBER] repeat MD simulations
Kanin Wichapong
(Sat May 18 2013 - 03:19:55 PDT)
Re: [AMBER] repeat MD simulations
Vlad Cojocaru
(Sat May 18 2013 - 04:34:24 PDT)
[AMBER] MMPBSA for stability analysis
Debayan Chakraborty
(Sat May 18 2013 - 10:43:21 PDT)
Re: [AMBER] MMPBSA for stability analysis
Jason Swails
(Sat May 18 2013 - 18:12:07 PDT)
[AMBER] Grid command for water density
BERGY
(Sun May 19 2013 - 02:08:08 PDT)
[AMBER] antechamber and sqm problem
Cenk \(Jenk\) Andac
(Sun May 19 2013 - 11:07:40 PDT)
Re: [AMBER] antechamber and sqm problem
Jason Swails
(Sun May 19 2013 - 12:26:31 PDT)
Re: [AMBER] Grid command for water density
Jason Swails
(Tue May 21 2013 - 04:49:55 PDT)
[AMBER] Molecular Shape Searching on GPUs
MARK
(Mon May 20 2013 - 11:05:45 PDT)
Re: [AMBER] Molecular Shape Searching on GPUs
MARK
(Mon May 20 2013 - 11:09:06 PDT)
[AMBER] cpptraj and avgcoord
Anselm Horn
(Tue May 21 2013 - 14:37:35 PDT)
Re: [AMBER] cpptraj and avgcoord
Daniel Roe
(Tue May 21 2013 - 16:03:01 PDT)
Re: [AMBER] cpptraj and avgcoord
Anselm Horn
(Wed May 22 2013 - 07:10:16 PDT)
[AMBER] JAC benchmark tests on K20X
Shan-ho Tsai
(Mon May 20 2013 - 12:00:16 PDT)
Re: [AMBER] JAC benchmark tests on K20X
Ross Walker
(Mon May 20 2013 - 12:21:49 PDT)
Re: [AMBER] JAC benchmark tests on K20X
Shan-ho Tsai
(Mon May 20 2013 - 13:11:13 PDT)
Re: [AMBER] JAC benchmark tests on K20X
Jason Swails
(Tue May 21 2013 - 04:32:31 PDT)
Re: [AMBER] JAC benchmark tests on K20X
Shan-ho Tsai
(Tue May 21 2013 - 07:05:05 PDT)
[AMBER] Qm/mm gaussian template=1
jcgt
(Tue May 21 2013 - 03:32:36 PDT)
Re: [AMBER] Qm/mm gaussian template=1
Andreas Goetz
(Tue May 21 2013 - 16:48:51 PDT)
Re: [AMBER] Qm/mm gaussian template=1
jcgt
(Wed May 22 2013 - 00:39:00 PDT)
Re: [AMBER] Qm/mm gaussian template=1
jcgt
(Thu May 23 2013 - 02:13:57 PDT)
Re: [AMBER] Qm/mm gaussian template=1
Andreas Goetz
(Thu May 23 2013 - 07:21:17 PDT)
[AMBER] how to remove the overlap between molecules
Rasha Alqus
(Tue May 21 2013 - 03:56:30 PDT)
Re: [AMBER] how to remove the overlap between molecules
Jason Swails
(Tue May 21 2013 - 04:44:38 PDT)
[AMBER] problem with parmchk and a big organic molecule
Rebeca García Fandiño
(Tue May 21 2013 - 05:29:04 PDT)
[AMBER] Energy and gradient inconsistent between AMBER and NAB
Chris Whittleston
(Tue May 21 2013 - 08:39:06 PDT)
Re: [AMBER] Energy and gradient inconsistent between AMBER and NAB
Jason Swails
(Tue May 21 2013 - 10:26:58 PDT)
[AMBER] How to construct a mol2 file from a PDB and RESP output files ?
ABEL Stephane 175950
(Wed May 22 2013 - 04:08:06 PDT)
Re: [AMBER] How to construct a mol2 file from a PDB and RESP output files ?
Ayesha Fatima
(Wed May 22 2013 - 05:25:41 PDT)
[AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ?
ABEL Stephane 175950
(Wed May 22 2013 - 05:52:54 PDT)
Re: [AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ?
Ayesha Fatima
(Wed May 22 2013 - 08:32:03 PDT)
Re: [AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ?
FyD
(Thu May 23 2013 - 04:53:21 PDT)
Re: [AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ?
Ayesha Fatima
(Thu May 23 2013 - 21:26:57 PDT)
Re: [AMBER] How to construct a mol2 file from a PDB and RESP output files ?
David A Case
(Wed May 22 2013 - 06:08:22 PDT)
[AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ?
ABEL Stephane 175950
(Wed May 22 2013 - 06:26:51 PDT)
Re: [AMBER] How to construct a mol2 file from a PDB and RESP output files ?
FyD
(Thu May 23 2013 - 03:49:05 PDT)
[AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ?
ABEL Stephane 175950
(Thu May 23 2013 - 03:55:16 PDT)
[AMBER] Energy and force blow up when I previously performe rmsd-fit for MD trajectory.
kurisaki
(Wed May 22 2013 - 05:04:14 PDT)
Re: [AMBER] Energy and force blow up when I previously performe rmsd-fit for MD trajectory.
Daniel Roe
(Wed May 22 2013 - 05:54:51 PDT)
Re: [AMBER] Energy and force blow up when I previously performe rmsd-fit for MD trajectory.
kurisaki
(Wed May 22 2013 - 06:11:15 PDT)
[AMBER] AMBERTOOLS: sqm fails to read input with more than 1000 external charges
Franz Symalla
(Wed May 22 2013 - 05:56:42 PDT)
Re: [AMBER] AMBERTOOLS: sqm fails to read input with more than 1000 external charges
Andreas Goetz
(Wed May 22 2013 - 14:28:21 PDT)
Re: [AMBER] AMBERTOOLS: sqm fails to read input with more than 1000 external charges
Franz Symalla
(Thu May 23 2013 - 03:12:22 PDT)
[AMBER] create prmtop strcuture file for sumoylated residues
crazylyf
(Wed May 22 2013 - 06:18:50 PDT)
[AMBER] TR : [PROVENANCE INTERNET] RE : How to construct a mol2 file from a PDB and RESP outputfiles ?
ABEL Stephane 175950
(Wed May 22 2013 - 06:31:43 PDT)
[AMBER] Query regarding mechanical unfolding of protein
Manish Paul
(Wed May 22 2013 - 11:22:12 PDT)
[AMBER] Relationship of time-autocorrelation plots for two lengths of time
Sajeewa Pemasinghe
(Wed May 22 2013 - 13:35:16 PDT)
Re: [AMBER] Relationship of time-autocorrelation plots for two lengths of time
George Giambasu
(Wed May 22 2013 - 14:20:07 PDT)
Re: [AMBER] Relationship of time-autocorrelation plots for two lengths of time
Sajeewa Pemasinghe
(Wed May 22 2013 - 14:28:27 PDT)
Re: [AMBER] Relationship of time-autocorrelation plots for two lengths of time
George Giambasu
(Thu May 23 2013 - 06:42:08 PDT)
Re: [AMBER] Relationship of time-autocorrelation plots for two lengths of time
Sajeewa Pemasinghe
(Thu May 23 2013 - 14:31:04 PDT)
[AMBER] Question about the normalization of velocity autocorrelation function
Sajeewa Pemasinghe
(Wed May 22 2013 - 15:15:59 PDT)
Re: [AMBER] Question about the normalization of velocity autocorrelation function
David A Case
(Thu May 23 2013 - 04:46:02 PDT)
Re: [AMBER] Question about the normalization of velocity autocorrelation function
Sajeewa Pemasinghe
(Thu May 23 2013 - 05:12:43 PDT)
[AMBER] Problem in updating AmberTools 12
Kshatresh Dutta Dubey
(Thu May 23 2013 - 06:33:03 PDT)
Re: [AMBER] Problem in updating AmberTools 12
Jason Swails
(Thu May 23 2013 - 15:32:25 PDT)
[AMBER] example karplus.txt file for cpptraj jcoupling command
Duggan, Brendan
(Thu May 23 2013 - 10:28:42 PDT)
Re: [AMBER] example karplus.txt file for cpptraj jcoupling command
Daniel Roe
(Thu May 23 2013 - 12:35:44 PDT)
Re: [AMBER] example karplus.txt file for cpptraj jcoupling command
Duggan, Brendan
(Fri May 24 2013 - 13:06:20 PDT)
Re: [AMBER] example karplus.txt file for cpptraj jcoupling command
Daniel Roe
(Fri May 24 2013 - 13:24:03 PDT)
Re: [AMBER] example karplus.txt file for cpptraj jcoupling command
Duggan, Brendan
(Fri May 31 2013 - 15:03:05 PDT)
Re: [AMBER] example karplus.txt file for cpptraj jcoupling command
Daniel Roe
(Fri May 31 2013 - 15:24:20 PDT)
[AMBER] GPU version availability on Gordon-SDSC and Kraken NICS
Senthil Natesan
(Thu May 23 2013 - 10:39:28 PDT)
Re: [AMBER] GPU version availability on Gordon-SDSC and Kraken NICS
Ross Walker
(Thu May 23 2013 - 10:45:27 PDT)
[AMBER] TI erro - atom coordinate disagreement
Kumar Sonu
(Thu May 23 2013 - 10:50:30 PDT)
Re: [AMBER] TI erro - atom coordinate disagreement
steinbrt.rci.rutgers.edu
(Thu May 23 2013 - 12:05:07 PDT)
[AMBER] SQM: How to extract the charge density of sqm runs?
Franz Symalla
(Thu May 23 2013 - 14:33:04 PDT)
Re: [AMBER] SQM: How to extract the charge density of sqm runs?
David A Case
(Fri May 24 2013 - 05:15:07 PDT)
Re: [AMBER] SQM: How to extract the charge density of sqm runs?
Andreas Goetz
(Fri May 24 2013 - 16:13:26 PDT)
[AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC
Jacob Monroe
(Thu May 23 2013 - 20:38:13 PDT)
Re: [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC
FyD
(Thu May 23 2013 - 23:56:28 PDT)
Re: [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC
David A Case
(Fri May 24 2013 - 05:11:12 PDT)
Re: [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC
Jacob Monroe
(Fri May 24 2013 - 13:02:49 PDT)
Re: [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC
David A Case
(Sat May 25 2013 - 05:30:20 PDT)
Re: [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC
Jacob Monroe
(Mon May 27 2013 - 09:07:44 PDT)
Re: [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC
FyD
(Sat May 25 2013 - 09:00:09 PDT)
[AMBER] About addIonsRand
Marc van der Kamp
(Fri May 24 2013 - 06:03:33 PDT)
[AMBER] Steered Molecular dynamics
Santi Tolosa
(Fri May 24 2013 - 10:01:42 PDT)
[AMBER] problem on compiling sander
me, Nancy
(Sat May 25 2013 - 11:41:16 PDT)
Re: [AMBER] problem on compiling sander
David A Case
(Sun May 26 2013 - 16:29:48 PDT)
Re: [AMBER] problem on compiling sander
me, Nancy
(Mon May 27 2013 - 09:40:31 PDT)
[AMBER] Chained AMBER jobs crash on Dual GPU compute node.
ET
(Sun May 26 2013 - 00:52:54 PDT)
Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node.
Jan-Philip Gehrcke
(Sun May 26 2013 - 11:30:10 PDT)
Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node.
ET
(Mon May 27 2013 - 03:41:40 PDT)
Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node.
Jan-Philip Gehrcke
(Mon May 27 2013 - 09:04:15 PDT)
Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node.
ET
(Tue May 28 2013 - 02:51:37 PDT)
Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node.
Jason Swails
(Wed May 29 2013 - 07:15:33 PDT)
Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node.
ET
(Wed May 29 2013 - 09:39:56 PDT)
Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node.
Jason Swails
(Wed May 29 2013 - 11:16:24 PDT)
Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node.
ET
(Thu May 30 2013 - 01:35:16 PDT)
[AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Mon May 27 2013 - 10:01:39 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Scott Le Grand
(Mon May 27 2013 - 16:25:24 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Mon May 27 2013 - 17:41:58 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Scott Le Grand
(Tue May 28 2013 - 07:59:33 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Robert Konecny
(Tue May 28 2013 - 08:11:47 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Gould, Ian R
(Tue May 28 2013 - 08:50:53 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Scott Le Grand
(Tue May 28 2013 - 08:57:33 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
ET
(Tue May 28 2013 - 11:42:32 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Scott Le Grand
(Tue May 28 2013 - 12:01:20 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Robert Konecny
(Tue May 28 2013 - 13:36:52 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Tue May 28 2013 - 12:24:36 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Scott Le Grand
(Tue May 28 2013 - 13:13:36 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Tue May 28 2013 - 13:20:45 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Scott Le Grand
(Tue May 28 2013 - 13:46:30 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
ET
(Tue May 28 2013 - 17:11:27 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Divi/GMAIL
(Tue May 28 2013 - 17:12:19 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
ET
(Tue May 28 2013 - 17:41:05 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Scott Le Grand
(Tue May 28 2013 - 17:49:31 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Ross Walker
(Tue May 28 2013 - 18:44:33 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Wed May 29 2013 - 13:11:12 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Scott Le Grand
(Wed May 29 2013 - 13:41:46 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Scott Le Grand
(Wed May 29 2013 - 13:46:58 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Wed May 29 2013 - 14:22:34 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Scott Le Grand
(Wed May 29 2013 - 16:05:24 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Wed May 29 2013 - 16:30:53 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Scott Le Grand
(Wed May 29 2013 - 17:46:59 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Wed May 29 2013 - 18:24:30 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Jason Swails
(Wed May 29 2013 - 13:44:18 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Wed May 29 2013 - 15:00:19 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Jason Swails
(Wed May 29 2013 - 19:42:10 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
ET
(Thu May 30 2013 - 01:33:13 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
ET
(Thu May 30 2013 - 05:08:18 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Thu May 30 2013 - 05:32:57 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
ET
(Thu May 30 2013 - 07:06:17 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Thu May 30 2013 - 07:49:27 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Scott Le Grand
(Thu May 30 2013 - 09:55:44 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
ET
(Thu May 30 2013 - 10:27:13 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Thu May 30 2013 - 05:14:55 PDT)
[AMBER] Sample LMOD program (nab section of AmberTools manual)
Chris Moth
(Thu May 30 2013 - 12:56:25 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
pavel.banas.upol.cz
(Thu May 30 2013 - 10:56:15 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Scott Le Grand
(Thu May 30 2013 - 11:01:58 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
filip fratev
(Thu May 30 2013 - 11:46:01 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Jason Swails
(Thu May 30 2013 - 12:13:29 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Scott Le Grand
(Thu May 30 2013 - 12:24:43 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Scott Le Grand
(Thu May 30 2013 - 12:27:17 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Thu May 30 2013 - 15:00:21 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Scott Le Grand
(Thu May 30 2013 - 15:45:49 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Thu May 30 2013 - 15:41:54 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
ET
(Fri May 31 2013 - 03:17:07 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
ET
(Fri May 31 2013 - 03:21:21 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Fri May 31 2013 - 03:29:59 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Fri May 31 2013 - 05:34:27 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
filip fratev
(Fri May 31 2013 - 08:30:57 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Fri May 31 2013 - 08:30:02 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Fri May 31 2013 - 08:40:01 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
ET
(Fri May 31 2013 - 10:17:03 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Fri May 31 2013 - 10:55:41 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
ET
(Fri May 31 2013 - 13:02:34 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
Marek Maly
(Fri May 31 2013 - 13:14:47 PDT)
Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ?
ET
(Fri May 31 2013 - 15:45:42 PDT)
[AMBER] atomicfluct
George Tzotzos
(Mon May 27 2013 - 10:34:10 PDT)
Re: [AMBER] atomicfluct
Daniel Roe
(Mon May 27 2013 - 12:13:18 PDT)
Re: [AMBER] atomicfluct
George Tzotzos
(Mon May 27 2013 - 12:28:18 PDT)
Re: [AMBER] atomicfluct
Daniel Roe
(Tue May 28 2013 - 08:30:30 PDT)
Re: [AMBER] atomicfluct
David A Case
(Tue May 28 2013 - 09:15:32 PDT)
[AMBER] Free energy calculation of pyridine
Bishnu Thapa
(Mon May 27 2013 - 14:35:58 PDT)
Re: [AMBER] Free energy calculation of pyridine
David A Case
(Mon May 27 2013 - 18:35:56 PDT)
[AMBER] About water flags running parm7 with NAMD
Francesco Pietra
(Tue May 28 2013 - 00:43:05 PDT)
Re: [AMBER] About water flags running parm7 with NAMD
Daniel Sindhikara
(Tue May 28 2013 - 02:08:58 PDT)
Re: [AMBER] About water flags running parm7 with NAMD
Francesco Pietra
(Tue May 28 2013 - 07:33:41 PDT)
Re: [AMBER] About water flags running parm7 with NAMD
Jason Swails
(Tue May 28 2013 - 07:55:19 PDT)
Re: [AMBER] About water flags running parm7 with NAMD
George Giambasu
(Tue May 28 2013 - 08:21:49 PDT)
Re: [AMBER] About water flags running parm7 with NAMD
Francesco Pietra
(Tue May 28 2013 - 08:42:21 PDT)
[AMBER] Cpptraj and hbonds
Fernando Martín García
(Tue May 28 2013 - 07:06:26 PDT)
Re: [AMBER] Cpptraj and hbonds
Daniel Roe
(Tue May 28 2013 - 07:33:43 PDT)
Re: [AMBER] Cpptraj and hbonds
Fernando Martín García
(Tue May 28 2013 - 07:36:56 PDT)
Re: [AMBER] Cpptraj and hbonds
Miguel Ortiz Lombardía
(Tue May 28 2013 - 07:56:42 PDT)
Re: [AMBER] Cpptraj and hbonds
Daniel Roe
(Tue May 28 2013 - 08:19:06 PDT)
Re: [AMBER] Cpptraj and hbonds
Miguel Ortiz Lombardía
(Tue May 28 2013 - 09:14:38 PDT)
[AMBER] GTX780
Fabrício Bracht
(Tue May 28 2013 - 10:36:58 PDT)
Re: [AMBER] GTX780
Scott Le Grand
(Tue May 28 2013 - 10:48:26 PDT)
[AMBER] Steered MD | Pulling Distance (between r2 and r2a in dist.RST file) is limitted to 100A | Offending restraint
Emmanuel
(Tue May 28 2013 - 12:29:54 PDT)
Re: [AMBER] Steered MD | Pulling Distance (between r2 and r2a in dist.RST file) is limitted to 100A | Offending restraint
Adrian Roitberg
(Tue May 28 2013 - 12:32:19 PDT)
Re: [AMBER] Steered MD | Pulling Distance (between r2 and r2a in dist.RST file) is limitted to 100A | Offending restraint
David A Case
(Tue May 28 2013 - 17:55:33 PDT)
[AMBER] Error message when using mpirun on amber12_parallel
肖立
(Thu May 30 2013 - 16:31:33 PDT)
Re: [AMBER] Error message when using mpirun on amber12_parallel
Jason Swails
(Thu May 30 2013 - 16:37:17 PDT)
Re: [AMBER] Error message when using mpirun on amber12_parallel
肖立
(Thu May 30 2013 - 16:47:04 PDT)
Re: [AMBER] Error message when using mpirun on amber12_parallel
Jason Swails
(Thu May 30 2013 - 19:33:28 PDT)
Re: [AMBER] Error message when using mpirun on amber12_parallel
肖立
(Thu May 30 2013 - 19:54:52 PDT)
Re: [AMBER] Error message when using mpirun on amber12_parallel
Mandal, Sanat
(Thu May 30 2013 - 16:52:40 PDT)
Re: [AMBER] AmberTools vs Amber
David A Case
(Fri May 31 2013 - 05:02:27 PDT)
Re: [AMBER] AmberTools vs Amber
Mandal, Sanat
(Fri May 31 2013 - 06:20:44 PDT)
[AMBER] FW: Trouble generating topology files
Teo, Theodosia Hua Swan - teohy004
(Thu May 30 2013 - 17:58:04 PDT)
Re: [AMBER] FW: Trouble generating topology files
David A Case
(Fri May 31 2013 - 05:08:24 PDT)
[AMBER] SMD calculation
Santi Tolosa
(Fri May 31 2013 - 03:00:40 PDT)
Re: [AMBER] SMD calculation
Jason Swails
(Fri May 31 2013 - 07:24:57 PDT)
[AMBER] reference group and pulled group in umbrella sampling
Jio M
(Fri May 31 2013 - 03:38:17 PDT)
[AMBER] by pmemd.cuda runs
Cenk \(Jenk\) Andac
(Fri May 31 2013 - 05:32:37 PDT)
Re: [AMBER] by pmemd.cuda runs
Marc van der Kamp
(Fri May 31 2013 - 06:12:46 PDT)
Re: [AMBER] by pmemd.cuda runs
Daniel Roe
(Fri May 31 2013 - 07:27:55 PDT)
Re: [AMBER] by pmemd.cuda runs
Moth, Chris
(Fri May 31 2013 - 09:09:03 PDT)
Re: [AMBER] by pmemd.cuda runs
Jason Swails
(Fri May 31 2013 - 11:11:01 PDT)
[AMBER] hbond in ptraj and cpptraj
pmaj.nencki.gov.pl
(Fri May 31 2013 - 06:14:21 PDT)
Re: [AMBER] hbond in ptraj and cpptraj
Daniel Roe
(Fri May 31 2013 - 07:24:00 PDT)
Last message date
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Fri May 31 2013 - 16:00:02 PDT
Archived on
: Fri Nov 22 2024 - 05:54:43 PST
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