Amber Archive May 2014: by subject

[AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable"
- Gustavo Seabra (Thu May 08 2014 - 06:10:58 PDT)
- Ross Walker (Thu May 08 2014 - 01:59:05 PDT)
- ahmed.sajid.stfc.ac.uk (Thu May 08 2014 - 01:31:07 PDT)
- ahmed.sajid.stfc.ac.uk (Thu May 08 2014 - 01:28:40 PDT)
- Ross Walker (Thu May 08 2014 - 00:00:46 PDT)
- ahmed.sajid.stfc.ac.uk (Wed May 07 2014 - 23:28:05 PDT)
- Scott Le Grand (Wed May 07 2014 - 10:31:16 PDT)
- Ross Walker (Wed May 07 2014 - 08:41:02 PDT)
- Jason Swails (Wed May 07 2014 - 04:37:55 PDT)
- ahmed.sajid.stfc.ac.uk (Wed May 07 2014 - 02:46:13 PDT)
[AMBER] 3NKB5
- 王珍 (Wed May 28 2014 - 18:17:00 PDT)
- Jason Swails (Wed May 28 2014 - 08:12:39 PDT)
- 王珍 (Wed May 28 2014 - 07:56:49 PDT)
- Jason Swails (Wed May 28 2014 - 07:29:13 PDT)
- 王珍 (Wed May 28 2014 - 07:19:11 PDT)
- 王珍 (Wed May 28 2014 - 06:00:20 PDT)
- Jason Swails (Tue May 27 2014 - 03:20:14 PDT)
- 王珍 (Tue May 27 2014 - 00:08:27 PDT)
[AMBER] Abdullahi Abubakar invited you to check out Dropbox
- Dropbox (Sun May 18 2014 - 18:58:02 PDT)
[AMBER] about GPU memory requirements
- Ross Walker (Wed May 14 2014 - 10:46:18 PDT)
- Daniel Roe (Wed May 14 2014 - 10:21:01 PDT)
- Thomas Evangelidis (Wed May 14 2014 - 02:41:15 PDT)
- Ross Walker (Tue May 13 2014 - 14:21:37 PDT)
- Thomas Evangelidis (Tue May 13 2014 - 14:12:13 PDT)
- Ross Walker (Mon May 12 2014 - 12:20:59 PDT)
- Jason Swails (Mon May 12 2014 - 12:14:32 PDT)
- Thomas Evangelidis (Mon May 12 2014 - 11:58:29 PDT)
[AMBER] About the chamber in Ambertools 14
- Yeng-Tseng Wang (Thu May 22 2014 - 21:34:04 PDT)
- Yeng-Tseng Wang (Thu May 22 2014 - 02:19:33 PDT)
- Ross Walker (Wed May 21 2014 - 20:31:09 PDT)
- Yeng-Tseng Wang (Wed May 21 2014 - 18:23:14 PDT)
[AMBER] About the reproducibility of pmemd
- Ross Walker (Mon May 19 2014 - 11:23:46 PDT)
- David A Case (Mon May 19 2014 - 05:50:13 PDT)
- Jason Swails (Mon May 19 2014 - 05:48:38 PDT)
- Val Yu (Mon May 19 2014 - 05:01:48 PDT)
[AMBER] Accelerated MD in Amber
- Christina Bergonzo (Wed May 28 2014 - 11:48:06 PDT)
- James Starlight (Wed May 28 2014 - 10:37:38 PDT)
- Daniel Roe (Wed May 28 2014 - 06:57:56 PDT)
- James Starlight (Wed May 28 2014 - 00:18:09 PDT)
- Daniel Roe (Tue May 27 2014 - 06:39:32 PDT)
- James Starlight (Sun May 25 2014 - 06:28:33 PDT)
[AMBER] acetylated lysine - OXT
- berin karaman (Fri May 16 2014 - 07:07:11 PDT)
- Jason Swails (Fri May 16 2014 - 06:46:03 PDT)
- berin karaman (Fri May 16 2014 - 05:39:00 PDT)
- David A Case (Fri May 16 2014 - 05:19:49 PDT)
- berin karaman (Fri May 16 2014 - 01:00:48 PDT)
[AMBER] acpype on ambertools13
- Alan (Mon May 05 2014 - 08:16:36 PDT)
- Jason Swails (Mon May 05 2014 - 04:18:57 PDT)
- Ahmet yıldırım (Mon May 05 2014 - 03:14:20 PDT)
- Jason Swails (Mon May 05 2014 - 03:08:31 PDT)
- Ahmet yıldırım (Mon May 05 2014 - 01:08:22 PDT)
[AMBER] Additional random motion of com for unwrapped trajectory
- Sourav Purohit (Tue May 20 2014 - 04:29:58 PDT)
- David A Case (Sun May 11 2014 - 06:00:34 PDT)
- Sourav Purohit (Sat May 10 2014 - 16:23:18 PDT)
[AMBER] ALA and NALA charges in Amber03 and Amber99
- Jason Swails (Wed May 21 2014 - 07:38:34 PDT)
- Rossen Apostolov (Wed May 21 2014 - 07:14:26 PDT)
- Jason Swails (Thu May 15 2014 - 09:00:47 PDT)
- Rossen Apostolov (Thu May 15 2014 - 08:44:19 PDT)
- Jason Swails (Thu May 15 2014 - 08:30:10 PDT)
- Rossen Apostolov (Thu May 15 2014 - 07:05:22 PDT)
[AMBER] alanine scanning
- Nitin Sharma (Sun May 04 2014 - 08:29:30 PDT)
- Bill Miller III (Sat May 03 2014 - 12:03:45 PDT)
- Nitin Sharma (Sat May 03 2014 - 06:47:35 PDT)
[AMBER] Alanine Scanning MMPBSA
- Jason Swails (Fri May 30 2014 - 08:16:22 PDT)
- Jason Swails (Fri May 30 2014 - 08:11:17 PDT)
- Jason Swails (Wed May 28 2014 - 06:52:26 PDT)
- Aronica, Pietro (Wed May 28 2014 - 06:36:07 PDT)
- Jason Swails (Tue May 20 2014 - 06:33:04 PDT)
- Aronica, Pietro (Tue May 20 2014 - 06:21:54 PDT)
- Aronica, Pietro (Tue May 13 2014 - 05:01:54 PDT)
- Jason Swails (Tue May 13 2014 - 04:27:13 PDT)
- Aronica, Pietro (Tue May 13 2014 - 04:06:08 PDT)
- Aronica, Pietro (Fri May 09 2014 - 06:01:57 PDT)
- Jason Swails (Fri May 09 2014 - 04:43:19 PDT)
- Aronica, Pietro (Fri May 09 2014 - 03:27:46 PDT)
- Jason Swails (Thu May 08 2014 - 10:19:36 PDT)
- Aronica, Pietro (Thu May 08 2014 - 10:08:13 PDT)
- Bill Miller III (Thu May 08 2014 - 09:50:33 PDT)
- Aronica, Pietro (Thu May 08 2014 - 09:45:12 PDT)
- Bill Miller III (Thu May 08 2014 - 09:12:22 PDT)
- Aronica, Pietro (Thu May 08 2014 - 08:56:28 PDT)
[AMBER] AMBER : mmpbsa rms in nmode
- Fengxue Li (Sat May 10 2014 - 05:54:29 PDT)
[AMBER] AMBER Digest, Vol 855, Issue 1
- Duggan, Brendan (Thu May 15 2014 - 12:18:17 PDT)
[AMBER] amber in namd
- amin.imtech.res.in (Fri May 30 2014 - 09:52:04 PDT)
- Jason Swails (Fri May 30 2014 - 08:58:12 PDT)
- Lara rajam (Fri May 30 2014 - 08:46:40 PDT)
- Jason Swails (Wed May 28 2014 - 08:41:54 PDT)
- Lara rajam (Wed May 28 2014 - 08:21:53 PDT)
[AMBER] AMBER Workshop Jun 2nd to 6th - Barcelona - Small number of additional places available.
- Ross Walker (Thu May 15 2014 - 12:03:04 PDT)
[AMBER] Amber workshops coming soon ?
- Saba Sulaiman (Sun May 11 2014 - 22:51:22 PDT)
[AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04
- David A Case (Sat May 10 2014 - 14:58:43 PDT)
- M. Reza Ganjalikhany (Sat May 10 2014 - 12:09:08 PDT)
- David A Case (Sat May 10 2014 - 05:30:40 PDT)
- M. Reza Ganjalikhany (Fri May 09 2014 - 23:09:08 PDT)
- David A Case (Wed May 07 2014 - 05:32:25 PDT)
- Jason Swails (Wed May 07 2014 - 05:04:37 PDT)
- M. Reza Ganjalikhany (Wed May 07 2014 - 01:32:52 PDT)
[AMBER] AmberTools 14 compilation on OSX fails
- Fabian Glaser (Thu May 15 2014 - 06:58:04 PDT)
- Jason Swails (Thu May 15 2014 - 06:23:35 PDT)
- Fabian Glaser (Thu May 15 2014 - 05:50:01 PDT)
- Fabian Glaser (Thu May 15 2014 - 05:44:34 PDT)
- Jason Swails (Thu May 15 2014 - 04:18:20 PDT)
- Fabian Glaser (Wed May 14 2014 - 22:42:11 PDT)
- Jason Swails (Wed May 14 2014 - 07:34:54 PDT)
- Fabian Glaser (Wed May 14 2014 - 06:44:44 PDT)
- Jason Swails (Wed May 14 2014 - 04:47:24 PDT)
- Fabian Glaser (Wed May 14 2014 - 01:48:08 PDT)
[AMBER] Analysis of evecs.dat file
- newamber list (Fri May 09 2014 - 10:52:11 PDT)
- Ibrahim Said (Fri May 09 2014 - 09:58:22 PDT)
[AMBER] Analysis of minimization stage
- Brian Radak (Tue May 20 2014 - 06:51:37 PDT)
- Valentina Romano (Tue May 20 2014 - 06:46:03 PDT)
- David A Case (Fri May 16 2014 - 17:46:14 PDT)
- Valentina Romano (Fri May 16 2014 - 06:50:49 PDT)
- Jason Swails (Fri May 16 2014 - 06:43:49 PDT)
- Valentina Romano (Fri May 16 2014 - 05:58:33 PDT)
- David A Case (Fri May 16 2014 - 05:26:34 PDT)
- Valentina Romano (Fri May 16 2014 - 04:39:19 PDT)
- Jason Swails (Thu May 15 2014 - 08:46:54 PDT)
- Daniel Roe (Thu May 15 2014 - 08:35:17 PDT)
- Valentina Romano (Thu May 15 2014 - 06:07:43 PDT)
- David A Case (Wed May 14 2014 - 08:01:13 PDT)
- Valentina Romano (Wed May 14 2014 - 06:58:08 PDT)
- Daniel Roe (Tue May 13 2014 - 08:58:07 PDT)
- Valentina Romano (Tue May 13 2014 - 07:30:41 PDT)
- Valentina Romano (Tue May 13 2014 - 07:02:11 PDT)
- Daniel Roe (Mon May 12 2014 - 11:00:40 PDT)
- Valentina Romano (Mon May 12 2014 - 09:26:44 PDT)
- Jason Swails (Mon May 12 2014 - 07:18:47 PDT)
- Valentina Romano (Mon May 12 2014 - 07:15:13 PDT)
- David A Case (Mon May 12 2014 - 06:59:47 PDT)
- Jason Swails (Mon May 12 2014 - 06:22:05 PDT)
- Valentina Romano (Mon May 12 2014 - 04:53:26 PDT)
- David A Case (Mon May 12 2014 - 04:47:04 PDT)
- Jason Swails (Mon May 12 2014 - 04:39:03 PDT)
- Valentina Romano (Mon May 12 2014 - 01:47:42 PDT)
- Valentina Romano (Fri May 09 2014 - 09:39:04 PDT)
- Daniel Roe (Fri May 09 2014 - 07:04:58 PDT)
- Valentina Romano (Fri May 09 2014 - 01:52:04 PDT)
- Daniel Roe (Thu May 08 2014 - 10:10:02 PDT)
- Valentina Romano (Thu May 08 2014 - 09:32:02 PDT)
- Daniel Roe (Thu May 08 2014 - 09:21:40 PDT)
- Asaminew Haile (Thu May 08 2014 - 09:13:57 PDT)
- Valentina Romano (Thu May 08 2014 - 09:04:41 PDT)
[AMBER] Analysis of the mmpbsa output
- Jason Swails (Wed May 14 2014 - 04:40:37 PDT)
- James Starlight (Wed May 14 2014 - 02:42:08 PDT)
- Jason Swails (Mon May 12 2014 - 04:52:22 PDT)
- James Starlight (Sun May 11 2014 - 00:43:44 PDT)
[AMBER] Announcement: New GLYCAM-Web
- Lachele Foley (Mon May 19 2014 - 14:40:55 PDT)
[AMBER] Antechamber
- CHRISTOPHER PATRICK MCNARY (Mon May 19 2014 - 08:18:03 PDT)
[AMBER] antechamber error
- Jason Swails (Thu May 22 2014 - 04:36:23 PDT)
- Sajda Ashraf (Thu May 22 2014 - 03:53:39 PDT)
[AMBER] antechamber with Au atom
- FyD (Mon May 19 2014 - 10:02:53 PDT)
- David A Case (Mon May 19 2014 - 04:50:41 PDT)
- giulia palermo (Mon May 19 2014 - 00:24:50 PDT)
[AMBER] Attempting to modify Amber
- David A Case (Thu May 22 2014 - 07:24:00 PDT)
- Nelson Max (Tue May 20 2014 - 17:47:39 PDT)
[AMBER] Bad prmtop during density run
- Jason Swails (Sat May 17 2014 - 10:46:22 PDT)
- Kshatresh Dutta Dubey (Sat May 17 2014 - 09:17:03 PDT)
[AMBER] can “NAB: Molecular mechanics and dynamics” do qmmm caculation?
- David A Case (Mon May 19 2014 - 04:51:22 PDT)
- 张明焜 (Mon May 19 2014 - 01:59:42 PDT)
[AMBER] cant run ntp=3 without csurften
- Ross Walker (Tue May 20 2014 - 13:27:33 PDT)
- Eric Hill (Tue May 20 2014 - 12:56:29 PDT)
- Ross Walker (Tue May 20 2014 - 12:24:49 PDT)
- Eric Hill (Tue May 20 2014 - 11:40:25 PDT)
- Benjamin D Madej (Tue May 20 2014 - 11:22:34 PDT)
- Benjamin D Madej (Tue May 20 2014 - 11:15:21 PDT)
- Jason Swails (Tue May 20 2014 - 10:11:40 PDT)
- Eric Hill (Tue May 20 2014 - 09:48:46 PDT)
[AMBER] command to check non bonded interactions like vander waal's interactions
- Soumendranath Bhakat (Wed May 28 2014 - 06:40:18 PDT)
- Jason Swails (Wed May 28 2014 - 06:37:26 PDT)
- Nitin Sharma (Wed May 28 2014 - 06:27:12 PDT)
[AMBER] compiling iAPBS and sander.APBS?
- Brian Radak (Tue May 27 2014 - 05:40:10 PDT)
- Robert Konecny (Sun May 25 2014 - 19:44:05 PDT)
- Brian Radak (Sun May 25 2014 - 08:17:43 PDT)
- Robert Konecny (Sat May 24 2014 - 19:54:28 PDT)
- Brian Radak (Fri May 23 2014 - 13:54:06 PDT)
[AMBER] Constant protein diffusion across PB boundaties
- Jason Swails (Tue May 20 2014 - 04:32:30 PDT)
- Jason Swails (Tue May 20 2014 - 04:30:41 PDT)
- James Starlight (Tue May 20 2014 - 01:59:22 PDT)
[AMBER] Contributing new water models
- David A Case (Wed May 28 2014 - 18:28:41 PDT)
- Lee-Ping Wang (Wed May 28 2014 - 12:26:43 PDT)
- Jason Swails (Wed May 28 2014 - 12:22:15 PDT)
- Lee-Ping Wang (Wed May 28 2014 - 11:35:30 PDT)
[AMBER] conversion force constant
- Jason Swails (Wed May 21 2014 - 05:25:42 PDT)
- giulia palermo (Wed May 21 2014 - 01:32:15 PDT)
- James Maier (Mon May 19 2014 - 12:44:22 PDT)
- giulia palermo (Mon May 19 2014 - 12:26:04 PDT)
[AMBER] creating quadruplex structure with NAB
- Ander (Thu May 08 2014 - 05:12:41 PDT)
[AMBER] csurften requirement for semiisotropic coupling
- Eric Hill (Tue May 20 2014 - 09:34:42 PDT)
[AMBER] Defining memory for QM/MM calculations
- Kshatresh Dutta Dubey (Thu May 08 2014 - 05:02:30 PDT)
- Jason Swails (Thu May 08 2014 - 04:29:23 PDT)
- Kshatresh Dutta Dubey (Thu May 08 2014 - 02:40:48 PDT)
[AMBER] delta Ggas and Delta Gsolv
- Jason Swails (Fri May 09 2014 - 06:40:53 PDT)
- Arunima Shilpi (Fri May 09 2014 - 06:31:29 PDT)
[AMBER] dihedrals in CYT residue
- Sidney Elmer (Tue May 06 2014 - 11:04:48 PDT)
- Jason Swails (Tue May 06 2014 - 10:33:28 PDT)
- Sidney Elmer (Tue May 06 2014 - 10:30:14 PDT)
- Sidney Elmer (Tue May 06 2014 - 10:04:16 PDT)
[AMBER] Disulfide Bond Info and XMIN Stuck Problems
- Guqin Shi (Thu May 29 2014 - 07:25:08 PDT)
- David A Case (Wed May 28 2014 - 16:55:31 PDT)
- Guqin Shi (Wed May 28 2014 - 14:05:21 PDT)
- David A Case (Wed May 28 2014 - 06:39:00 PDT)
- Guqin Shi (Tue May 27 2014 - 19:34:59 PDT)
- David A Case (Tue May 27 2014 - 17:25:07 PDT)
- Guqin Shi (Tue May 27 2014 - 09:14:29 PDT)
[AMBER] Empirical force fields: release new version of RED Server Dev/PyRED
- Marek Maly (Wed May 07 2014 - 12:13:45 PDT)
- FyD (Wed May 07 2014 - 11:38:09 PDT)
- Marek Maly (Wed May 07 2014 - 09:22:40 PDT)
- FyD (Wed May 07 2014 - 08:05:26 PDT)
- Marek Maly (Tue May 06 2014 - 15:06:49 PDT)
- FyD (Mon May 05 2014 - 23:22:33 PDT)
- Marek Maly (Mon May 05 2014 - 06:22:56 PDT)
- FyD (Mon May 05 2014 - 04:00:11 PDT)
[AMBER] error in equilibration
- Jason Swails (Wed May 07 2014 - 07:21:29 PDT)
- Lara rajam (Wed May 07 2014 - 07:03:23 PDT)
[AMBER] error in mdcrd file
- Sajda Ashraf (Tue May 20 2014 - 22:48:42 PDT)
[AMBER] error in minimization
- David A Case (Mon May 19 2014 - 04:48:54 PDT)
- Sajda Ashraf (Sun May 18 2014 - 22:21:02 PDT)
- David A Case (Sat May 17 2014 - 12:50:32 PDT)
- Sajda Ashraf (Fri May 16 2014 - 23:48:21 PDT)
[AMBER] error in plot of interaction energy in xmgrace
- Soumendranath Bhakat (Sat May 31 2014 - 06:54:53 PDT)
- Arunima Shilpi (Sat May 31 2014 - 06:03:22 PDT)
[AMBER] Error in setting irest=1
- Soumendranath Bhakat (Wed May 21 2014 - 00:19:58 PDT)
- Daniel Roe (Tue May 20 2014 - 09:39:29 PDT)
- Valentina Romano (Tue May 20 2014 - 09:14:07 PDT)
[AMBER] Error when using PB implicit solvent in XMIN in NAB(PB Bomb in pb_init(): Allocation aborted)
- Guqin Shi (Fri May 09 2014 - 13:42:58 PDT)
- Guqin Shi (Fri May 09 2014 - 13:35:50 PDT)
- David A Case (Fri May 09 2014 - 12:47:10 PDT)
- Ray Luo, Ph.D. (Fri May 09 2014 - 12:19:28 PDT)
- Guqin Shi (Fri May 09 2014 - 11:44:03 PDT)
[AMBER] Error: Could not compile with NetCDF Fortran interface gfortran-4.7 and amber14
- Daniel Roe (Thu May 15 2014 - 08:19:30 PDT)
- Ben.Cossins.ucb.com (Thu May 15 2014 - 04:22:44 PDT)
[AMBER] Error: invalid argument launching kernel kNLGenerateSpatialHash
- Ross Walker (Thu May 08 2014 - 02:00:50 PDT)
- ASFARINA AMIR HASSAN (Thu May 08 2014 - 01:31:27 PDT)
[AMBER] exctracting indivdual frames into seperate files
- Nitin Sharma (Tue May 13 2014 - 07:01:39 PDT)
- Jason Swails (Tue May 13 2014 - 07:00:54 PDT)
- Nitin Sharma (Tue May 13 2014 - 06:40:56 PDT)
- Jason Swails (Tue May 13 2014 - 06:01:19 PDT)
- Nitin Sharma (Tue May 13 2014 - 05:54:09 PDT)
[AMBER] Extending MMPBSA
- Bill Miller III (Sat May 17 2014 - 05:01:18 PDT)
- Arun Kumar Somavarapu (Sat May 17 2014 - 04:50:44 PDT)
[AMBER] Extract MD co-ordinates
- Jason Swails (Mon May 05 2014 - 10:56:45 PDT)
- Soumendranath Bhakat (Mon May 05 2014 - 10:28:42 PDT)
- Daniel Roe (Mon May 05 2014 - 09:27:24 PDT)
- Soumendranath Bhakat (Mon May 05 2014 - 07:19:14 PDT)
[AMBER] Extract velocity from the restart file
- Yin, Guowei (Mon May 05 2014 - 07:16:27 PDT)
- Jason Swails (Mon May 05 2014 - 07:13:10 PDT)
- Yin, Guowei (Mon May 05 2014 - 06:39:17 PDT)
[AMBER] FapydG parameters
- Norbert GARNIER (Wed May 07 2014 - 07:02:58 PDT)
- Carlos Simmerling (Wed May 07 2014 - 06:54:04 PDT)
- Christina Bergonzo (Wed May 07 2014 - 06:51:25 PDT)
- Norbert GARNIER (Wed May 07 2014 - 05:30:27 PDT)
[AMBER] ff99SB-ildn-nmr
- Jason Swails (Sat May 31 2014 - 11:59:30 PDT)
- Nihal Korkmaz (Sat May 31 2014 - 11:44:23 PDT)
[AMBER] Force field of antechamber , parm94 ? parm99?
- Jason Swails (Tue May 13 2014 - 04:40:07 PDT)
- Jinfeng Huang (Tue May 13 2014 - 03:14:48 PDT)
- Jason Swails (Mon May 12 2014 - 07:56:35 PDT)
- Jinfeng Huang (Mon May 12 2014 - 07:24:58 PDT)
- David A Case (Mon May 12 2014 - 04:52:04 PDT)
- Jason Swails (Mon May 12 2014 - 04:32:58 PDT)
- Jinfeng Huang (Mon May 12 2014 - 02:22:57 PDT)
[AMBER] Fwd: MMPBSA
- Soumya Lipsa Rath (Tue May 20 2014 - 06:36:39 PDT)
- Jason Swails (Tue May 20 2014 - 05:45:04 PDT)
- Soumya Lipsa Rath (Tue May 20 2014 - 04:49:27 PDT)
- Jason Swails (Tue May 20 2014 - 04:28:21 PDT)
- Soumya Lipsa Rath (Mon May 19 2014 - 21:31:29 PDT)
- Jason Swails (Mon May 19 2014 - 05:55:18 PDT)
- Soumya Lipsa Rath (Sun May 18 2014 - 22:19:18 PDT)
[AMBER] get sqm Error when run antechamber
- Biao Ma (Fri May 16 2014 - 00:38:46 PDT)
- David A Case (Thu May 15 2014 - 04:52:00 PDT)
- Biao Ma (Wed May 14 2014 - 19:36:16 PDT)
- Jason Swails (Wed May 14 2014 - 07:48:34 PDT)
- Biao Ma (Wed May 14 2014 - 07:24:41 PDT)
- Daniel Roe (Tue May 13 2014 - 10:36:37 PDT)
- liu junjun (Tue May 13 2014 - 03:32:46 PDT)
- Biao Ma (Mon May 12 2014 - 23:44:04 PDT)
[AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure."
- Ross Walker (Fri May 30 2014 - 08:42:42 PDT)
- Keiran Rowell (Thu May 29 2014 - 22:43:53 PDT)
[AMBER] handling long trajs for PCA and components plot
- newamber list (Wed May 21 2014 - 14:07:02 PDT)
- Daniel Roe (Mon May 19 2014 - 09:33:03 PDT)
- Daniel Roe (Mon May 12 2014 - 10:28:25 PDT)
- newamber list (Sun May 11 2014 - 12:10:13 PDT)
- Daniel Roe (Thu May 08 2014 - 08:04:14 PDT)
- newamber list (Wed May 07 2014 - 15:27:25 PDT)
- Daniel Roe (Wed May 07 2014 - 07:52:12 PDT)
- newamber list (Tue May 06 2014 - 21:21:41 PDT)
- Daniel Roe (Tue May 06 2014 - 20:27:07 PDT)
- newamber list (Tue May 06 2014 - 19:13:37 PDT)
- Daniel Roe (Tue May 06 2014 - 10:24:53 PDT)
- David A Case (Mon May 05 2014 - 18:26:09 PDT)
- newamber list (Mon May 05 2014 - 16:23:26 PDT)
[AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions
- Ben Ahmady (Mon May 19 2014 - 02:04:01 PDT)
- Ben Ahmady (Sun May 18 2014 - 13:43:45 PDT)
- Jason Swails (Fri May 16 2014 - 20:56:16 PDT)
- Jason Swails (Fri May 16 2014 - 20:50:53 PDT)
- Brian Radak (Fri May 16 2014 - 10:53:56 PDT)
- Ben Ahmady (Fri May 16 2014 - 09:40:04 PDT)
- Brian Radak (Fri May 16 2014 - 07:45:58 PDT)
- Ben Ahmady (Fri May 16 2014 - 07:29:42 PDT)
[AMBER] How to define the direction of the force in SMD method?
- Cuiyl (Mon May 26 2014 - 23:10:08 PDT)
- Jason Swails (Mon May 26 2014 - 12:36:08 PDT)
- Cuiyl (Sun May 25 2014 - 19:14:08 PDT)
[AMBER] How to extract each frame of a trajectory as individual .mdcrd files?
- Yew Mun Yip (Wed Apr 30 2014 - 09:05:39 PDT)
[AMBER] how to generate a complete amino acid in suitable for the vacuum simulation
- FyD (Wed May 07 2014 - 08:10:38 PDT)
- David A Case (Wed May 07 2014 - 05:13:18 PDT)
- 张明焜 (Tue May 06 2014 - 20:38:49 PDT)
[AMBER] How to plot Eigenvectors against % Positional Fluctuations
- Daniel Roe (Mon May 19 2014 - 07:24:14 PDT)
- Yip Yew Mun (Fri May 16 2014 - 21:09:18 PDT)
[AMBER] how to protonate phosphate groups of nucleotides
- FyD (Thu May 29 2014 - 00:08:35 PDT)
- Valentina D'Atri (Wed May 28 2014 - 08:59:37 PDT)
- FyD (Sun May 04 2014 - 22:19:14 PDT)
[AMBER] I want to know about formula of RESP Charge in the Amber
- Kim TaeHwan (Sat May 24 2014 - 08:43:39 PDT)
[AMBER] in vacuo dynamics
- Massimiliano Porrini (Tue May 27 2014 - 06:40:46 PDT)
- Jason Swails (Tue May 27 2014 - 06:19:37 PDT)
- Massimiliano Porrini (Tue May 27 2014 - 06:04:49 PDT)
- Robert McGibbon (Mon May 26 2014 - 14:09:13 PDT)
- Jason Swails (Mon May 26 2014 - 12:30:48 PDT)
- Jason Swails (Mon May 26 2014 - 12:21:59 PDT)
- Massimiliano Porrini (Mon May 26 2014 - 03:34:20 PDT)
- Robert McGibbon (Sun May 25 2014 - 12:30:49 PDT)
- Massimiliano Porrini (Sun May 25 2014 - 06:42:50 PDT)
- Jason Swails (Fri May 23 2014 - 07:41:01 PDT)
- Massimiliano Porrini (Fri May 23 2014 - 07:06:00 PDT)
- Jason Swails (Fri May 23 2014 - 05:11:58 PDT)
- Massimiliano Porrini (Fri May 23 2014 - 03:30:37 PDT)
- Massimiliano Porrini (Fri May 23 2014 - 03:18:44 PDT)
- Jason Swails (Thu May 22 2014 - 14:42:36 PDT)
- Massimiliano Porrini (Thu May 22 2014 - 12:52:26 PDT)
[AMBER] Inputs QM/MM MD and MMGBSA
- Soumendranath Bhakat (Sun May 11 2014 - 12:57:16 PDT)
[AMBER] Installation AmberTools13
- Jason Swails (Thu May 15 2014 - 04:07:04 PDT)
- fabien.ibanez.modis.fr.netgrs.com (Thu May 15 2014 - 01:24:13 PDT)
- fabien.ibanez.modis.fr.netgrs.com (Tue May 13 2014 - 07:30:53 PDT)
[AMBER] Installation of AmberTools13
- Jason Swails (Mon May 05 2014 - 08:47:58 PDT)
- fabien.ibanez.modis.fr.netgrs.com (Mon May 05 2014 - 08:11:56 PDT)
[AMBER] Installation Problem of AmberTools14
- Jason Swails (Wed May 14 2014 - 07:42:28 PDT)
- ujihara.ryuuta.47u.st.kyoto-u.ac.jp (Wed May 14 2014 - 06:09:41 PDT)
- Jason Swails (Wed May 14 2014 - 04:45:29 PDT)
- ujihara.ryuuta.47u.st.kyoto-u.ac.jp (Tue May 13 2014 - 21:54:10 PDT)
[AMBER] Interactions across the periodic box boundaries
- Jason Swails (Wed May 21 2014 - 14:45:52 PDT)
- Daniel Roe (Wed May 21 2014 - 14:00:48 PDT)
- Eugene Yedvabny (Wed May 21 2014 - 12:19:40 PDT)
[AMBER] Intermittent error during T-REMD on 8 GPU computer
- Milo Westler (Fri May 02 2014 - 08:33:05 PDT)
- Jason Swails (Fri May 02 2014 - 08:16:20 PDT)
- Milo Westler (Fri May 02 2014 - 07:33:48 PDT)
[AMBER] Loop refirement
- Vlad Cojocaru (Wed May 28 2014 - 00:53:40 PDT)
- James Starlight (Wed May 28 2014 - 00:29:44 PDT)
- James Starlight (Mon May 26 2014 - 03:06:13 PDT)
[AMBER] Low energy path
- Hector A. Baldoni (Wed May 21 2014 - 15:22:10 PDT)
- James Maier (Wed May 21 2014 - 07:07:22 PDT)
- Hector A. Baldoni (Wed May 21 2014 - 05:40:27 PDT)
[AMBER] MD at constant pH and high temperature
- Sangita Kachhap (Tue May 27 2014 - 09:13:12 PDT)
- Jason Swails (Mon May 26 2014 - 12:10:07 PDT)
- Sangita Kachhap (Mon May 26 2014 - 10:42:49 PDT)
- Adrian Roitberg (Mon May 26 2014 - 07:18:31 PDT)
- Sangita Kachhap (Mon May 26 2014 - 07:47:52 PDT)
- David A Case (Mon May 26 2014 - 06:58:36 PDT)
- Sangita Kachhap (Sun May 25 2014 - 06:48:41 PDT)
[AMBER] MD at constant pH and high temperature. .
- Sangita Kachhap (Mon May 26 2014 - 09:09:05 PDT)
- Bharatham, Nagakumar (Mon May 26 2014 - 08:48:21 PDT)
[AMBER] MD at pH5 and 50-55 degree celcius
- Sangita Kachhap (Tue May 27 2014 - 09:12:11 PDT)
- Daniel Roe (Tue May 27 2014 - 06:42:11 PDT)
- Sangita Kachhap (Sun May 25 2014 - 23:47:28 PDT)
[AMBER] Membrane protein simulation
- Ross Walker (Thu May 08 2014 - 00:04:46 PDT)
- James Starlight (Wed May 07 2014 - 23:50:22 PDT)
- Jason Swails (Tue May 06 2014 - 04:57:52 PDT)
- James Starlight (Tue May 06 2014 - 03:15:29 PDT)
[AMBER] MMPBSA
- Hallel Freedman (Thu May 29 2014 - 16:59:53 PDT)
- Ray Luo, Ph.D. (Thu May 29 2014 - 15:53:02 PDT)
- Hallel Freedman (Thu May 29 2014 - 15:22:03 PDT)
- Jason Swails (Thu May 29 2014 - 12:40:20 PDT)
- Hallel Freedman (Thu May 29 2014 - 12:28:07 PDT)
- Jason Swails (Thu May 29 2014 - 12:07:09 PDT)
- Hallel Freedman (Thu May 29 2014 - 11:34:28 PDT)
- Ray Luo, Ph.D. (Thu May 29 2014 - 09:44:56 PDT)
- Hallel Freedman (Wed May 28 2014 - 19:33:00 PDT)
- Hallel Freedman (Wed May 28 2014 - 16:23:25 PDT)
- Ray Luo, Ph.D. (Wed May 28 2014 - 16:22:04 PDT)
- Hallel Freedman (Wed May 28 2014 - 11:54:19 PDT)
- Hallel Freedman (Wed May 28 2014 - 11:13:17 PDT)
- Ray Luo, Ph.D. (Tue May 27 2014 - 12:41:24 PDT)
- Hallel Freedman (Tue May 27 2014 - 11:05:32 PDT)
- Lara rajam (Thu May 22 2014 - 11:41:16 PDT)
- Jason Swails (Thu May 22 2014 - 08:31:53 PDT)
- zahra khatti (Thu May 22 2014 - 07:59:23 PDT)
- Soumendranath Bhakat (Sat May 17 2014 - 05:48:50 PDT)
- Bill Miller III (Sat May 17 2014 - 04:11:43 PDT)
- Soumya Lipsa Rath (Sat May 17 2014 - 03:04:38 PDT)
[AMBER] MMPBSA & mmpbsa_py_nabnmode frequent crashes
- Jason Swails (Tue May 06 2014 - 18:53:01 PDT)
- Amir Shahmoradi (Tue May 06 2014 - 17:07:45 PDT)
[AMBER] MMPBSA: Per Residue vs Pairwise decomposition Calculation
- Rodriguez, Yoel (Mon May 26 2014 - 18:01:44 PDT)
[AMBER] MMPBSA: Per Residue vs Pairwise decomposition Calculation(idecomp= 2 o idecomp=4)
- Rodriguez, Yoel (Tue May 27 2014 - 10:22:06 PDT)
[AMBER] mmpbsa: the nmode calculation
- Fengxue Li (Thu May 08 2014 - 23:11:07 PDT)
- Fengxue Li (Thu May 08 2014 - 06:41:53 PDT)
[AMBER] MMPBSA_complex.mdcrd.0 error
- Ray Luo, Ph.D. (Thu May 29 2014 - 10:01:30 PDT)
- mahnam karim (Thu May 29 2014 - 07:03:58 PDT)
[AMBER] Modeling systems with non-standard residues
- James Starlight (Tue May 13 2014 - 04:41:03 PDT)
- Jason Swails (Mon May 12 2014 - 04:41:33 PDT)
- Parker de Waal (Mon May 12 2014 - 04:31:30 PDT)
- James Starlight (Mon May 12 2014 - 00:05:54 PDT)
- Brent Krueger (Sun May 11 2014 - 05:35:29 PDT)
- James Starlight (Sun May 11 2014 - 03:24:39 PDT)
- Jason Swails (Thu May 08 2014 - 04:17:18 PDT)
- FyD (Thu May 08 2014 - 04:08:52 PDT)
- James Starlight (Wed May 07 2014 - 23:43:15 PDT)
[AMBER] multinode NPT runs on GPU
- Brian Radak (Fri May 09 2014 - 09:04:14 PDT)
- Jason Swails (Fri May 09 2014 - 08:32:56 PDT)
- Sourav Purohit (Fri May 09 2014 - 07:19:06 PDT)
- Jason Swails (Fri May 09 2014 - 07:00:29 PDT)
- Sourav Purohit (Fri May 09 2014 - 06:43:59 PDT)
- Jason Swails (Fri May 09 2014 - 06:34:56 PDT)
- Sourav Purohit (Fri May 09 2014 - 05:50:19 PDT)
[AMBER] Need help as a beginner
- Jason Swails (Wed May 14 2014 - 05:52:21 PDT)
- MURAT OZTURK (Wed May 14 2014 - 05:44:08 PDT)
- MURAT OZTURK (Wed May 14 2014 - 05:42:54 PDT)
- Jason Swails (Wed May 14 2014 - 05:25:09 PDT)
- MURAT OZTURK (Tue May 13 2014 - 16:02:53 PDT)
- Jason Swails (Tue May 13 2014 - 15:16:57 PDT)
- Ilyas Yildirim (Tue May 13 2014 - 13:48:59 PDT)
- MURAT OZTURK (Tue May 13 2014 - 13:47:35 PDT)
- David A Case (Tue May 13 2014 - 13:28:33 PDT)
- MURAT OZTURK (Tue May 13 2014 - 13:17:49 PDT)
- Ilyas Yildirim (Tue May 13 2014 - 12:46:24 PDT)
- MURAT OZTURK (Tue May 13 2014 - 12:31:59 PDT)
[AMBER] NH4+
- Alessandro Contini (Wed May 21 2014 - 01:19:19 PDT)
- Thomas Exner (Wed May 21 2014 - 01:15:26 PDT)
- FyD (Mon May 19 2014 - 09:59:40 PDT)
- Alessandro Contini (Mon May 19 2014 - 06:29:00 PDT)
- Thomas Exner (Mon May 19 2014 - 06:00:21 PDT)
- Alessandro Contini (Mon May 19 2014 - 05:54:24 PDT)
- Thomas Exner (Mon May 19 2014 - 05:31:56 PDT)
[AMBER] number of frames in MMPBGBSA
- Soumendranath Bhakat (Tue May 06 2014 - 11:17:02 PDT)
- Nitin Sharma (Tue May 06 2014 - 08:38:06 PDT)
- Soumendranath Bhakat (Tue May 06 2014 - 08:22:44 PDT)
- Bill Miller III (Tue May 06 2014 - 07:29:07 PDT)
- Nitin Sharma (Tue May 06 2014 - 05:15:24 PDT)
[AMBER] Pairwise interaction energy between each residue
- Jason Swails (Tue May 06 2014 - 07:26:24 PDT)
- MOHD HOMAIDUR RAHMAN (Tue May 06 2014 - 00:28:04 PDT)
[AMBER] pairwise option in cpptraj
- Daniel Roe (Thu May 15 2014 - 14:06:58 PDT)
- newamber list (Thu May 15 2014 - 12:14:40 PDT)
- Daniel Roe (Thu May 15 2014 - 11:15:09 PDT)
- newamber list (Thu May 15 2014 - 10:25:28 PDT)
[AMBER] Parameters for FAD
- Jason Swails (Fri May 02 2014 - 04:40:01 PDT)
- amin.imtech.res.in (Thu May 01 2014 - 22:19:09 PDT)
- Jason Swails (Thu May 01 2014 - 12:20:38 PDT)
- amin.imtech.res.in (Thu May 01 2014 - 12:05:44 PDT)
- ABEL Stephane 175950 (Thu May 01 2014 - 06:37:41 PDT)
- amin.imtech.res.in (Thu May 01 2014 - 06:26:59 PDT)
[AMBER] Parametrization of non-standart residues
- Jason Swails (Sat May 31 2014 - 07:53:51 PDT)
- FyD (Sat May 31 2014 - 06:54:48 PDT)
- James Starlight (Sat May 31 2014 - 06:21:30 PDT)
- Parker de Waal (Sat May 31 2014 - 05:50:12 PDT)
- James Starlight (Sat May 31 2014 - 04:50:56 PDT)
- FyD (Sat May 31 2014 - 01:11:00 PDT)
- James Starlight (Fri May 30 2014 - 23:07:39 PDT)
- Parker de Waal (Fri May 30 2014 - 12:43:16 PDT)
- James Starlight (Fri May 30 2014 - 12:04:01 PDT)
- James Starlight (Fri May 30 2014 - 12:00:14 PDT)
- Jason Swails (Fri May 30 2014 - 11:25:47 PDT)
- James Starlight (Fri May 30 2014 - 11:12:33 PDT)
[AMBER] parmchk2 segfaults
- Hannes Loeffler (Fri May 16 2014 - 06:50:54 PDT)
[AMBER] pbsa: solvation radius from topology file not used when radiopt=0
- Ray Luo, Ph.D. (Sat May 24 2014 - 11:52:15 PDT)
- Jan-Philip Gehrcke (Sat May 24 2014 - 10:37:25 PDT)
[AMBER] PCA and the corresponding pdb
- Daniel Roe (Wed May 28 2014 - 06:37:39 PDT)
- Soumendranath Bhakat (Wed May 28 2014 - 01:08:31 PDT)
- Daniel Roe (Tue May 27 2014 - 13:39:36 PDT)
- Ibrahim Said (Tue May 27 2014 - 13:32:12 PDT)
- Daniel Roe (Tue May 27 2014 - 06:49:39 PDT)
- Ibrahim Said (Mon May 26 2014 - 11:54:38 PDT)
[AMBER] PDB for 1-octanol molecules
- FyD (Wed May 07 2014 - 08:13:05 PDT)
- David A Case (Wed May 07 2014 - 05:17:09 PDT)
- Jason Swails (Wed May 07 2014 - 04:55:04 PDT)
- Mari Mak (Tue May 06 2014 - 23:13:18 PDT)
[AMBER] Peptides moving out of the water box
- Daniel Roe (Wed May 21 2014 - 07:01:20 PDT)
- Ilias Patmanidis (Wed May 21 2014 - 06:47:39 PDT)
[AMBER] Percent Occupancey with PCA
- Nicole Ippolito (Mon May 05 2014 - 08:28:27 PDT)
- Daniel Roe (Sat May 03 2014 - 00:11:50 PDT)
- Nicole Ippolito (Fri May 02 2014 - 08:17:34 PDT)
[AMBER] Percent Occupancy with PCA
- Jason Swails (Mon May 05 2014 - 08:50:50 PDT)
- Nicole Ippolito (Mon May 05 2014 - 08:25:26 PDT)
[AMBER] periodic box buffer zone
- Brian Radak (Fri May 30 2014 - 08:52:19 PDT)
- Paulsen, Janet (Fri May 30 2014 - 08:35:34 PDT)
[AMBER] please let me unsubscribe of this
- Jason Swails (Thu May 08 2014 - 04:12:46 PDT)
- adm (Wed May 07 2014 - 23:31:28 PDT)
[AMBER] pmemd.MPI failure
- James Maier (Fri May 09 2014 - 11:18:28 PDT)
- George Tzotzos (Fri May 09 2014 - 10:59:53 PDT)
[AMBER] PMF as a function of Q, fraction of native contacts
- Adrian Roitberg (Tue May 06 2014 - 06:59:29 PDT)
- Brian Radak (Tue May 06 2014 - 06:51:02 PDT)
- Carlos Simmerling (Mon May 05 2014 - 16:25:58 PDT)
- Nihal Korkmaz (Mon May 05 2014 - 15:47:13 PDT)
[AMBER] Prepareing branched residue
- FyD (Wed May 07 2014 - 12:05:34 PDT)
- kurisaki (Tue May 06 2014 - 19:19:04 PDT)
- FyD (Sun May 04 2014 - 23:47:14 PDT)
- kurisaki (Thu May 01 2014 - 22:57:23 PDT)
[AMBER] print residue
- Soumendranath Bhakat (Wed May 28 2014 - 23:40:33 PDT)
- Arunima Shilpi (Wed May 28 2014 - 22:07:29 PDT)
- Soumendranath Bhakat (Wed May 28 2014 - 05:15:18 PDT)
- Jason Swails (Wed May 28 2014 - 05:03:20 PDT)
- Arunima Shilpi (Tue May 27 2014 - 22:07:04 PDT)
[AMBER] prmtop error
- Jason Swails (Thu May 22 2014 - 19:15:38 PDT)
- Thomas Cheatham (Thu May 22 2014 - 15:07:07 PDT)
- Jason Swails (Thu May 22 2014 - 14:45:39 PDT)
- Soumendranath Bhakat (Thu May 22 2014 - 12:42:25 PDT)
- Lara rajam (Thu May 22 2014 - 12:08:41 PDT)
[AMBER] Problem in generating xml param files
- Sushi Shilpa (Fri May 16 2014 - 23:06:18 PDT)
[AMBER] Problem in loading leaprc.zinc
- amin.imtech.res.in (Fri May 23 2014 - 06:55:55 PDT)
- Jason Swails (Fri May 23 2014 - 05:23:57 PDT)
- amin.imtech.res.in (Thu May 22 2014 - 23:05:06 PDT)
[AMBER] Problem in parallel version of pmemd.cuda
- Jason Swails (Tue May 20 2014 - 10:04:39 PDT)
- Sanjib Paul (Tue May 20 2014 - 09:32:09 PDT)
- Jason Swails (Tue May 20 2014 - 08:31:41 PDT)
- Sanjib Paul (Tue May 20 2014 - 08:23:29 PDT)
- Daniel Roe (Tue May 20 2014 - 07:23:47 PDT)
- Jason Swails (Tue May 20 2014 - 06:40:37 PDT)
- Sanjib Paul (Tue May 20 2014 - 06:26:59 PDT)
- David A Case (Mon May 19 2014 - 13:58:45 PDT)
- Ross Walker (Mon May 19 2014 - 11:25:59 PDT)
- Sanjib Paul (Mon May 19 2014 - 11:16:41 PDT)
[AMBER] Problem in restarting simulation from restart file
- Jason Swails (Fri May 30 2014 - 05:44:50 PDT)
- Kshatresh Dutta Dubey (Fri May 30 2014 - 05:04:59 PDT)
[AMBER] problem using pmemd.cuda with barostat=2 option
- Asaminew Haile (Sat May 31 2014 - 09:01:30 PDT)
- Jason Swails (Sat May 31 2014 - 08:51:25 PDT)
- Asaminew Haile (Sat May 31 2014 - 08:10:50 PDT)
[AMBER] Problem with Decomposition of Binding Free Energy
- Jason Swails (Fri May 16 2014 - 21:06:05 PDT)
- loue chen (Fri May 16 2014 - 12:08:46 PDT)
[AMBER] problem with nmode
- David A Case (Mon May 12 2014 - 04:49:44 PDT)
- Fengxue Li (Mon May 12 2014 - 01:54:07 PDT)
[AMBER] Problem with the amber-14 compilation on Debian
- Jason Swails (Tue May 06 2014 - 07:55:47 PDT)
- James Starlight (Tue May 06 2014 - 07:04:22 PDT)
- Jason Swails (Tue May 06 2014 - 05:05:15 PDT)
- James Starlight (Tue May 06 2014 - 00:09:37 PDT)
[AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670
- Josh Berryman (Thu May 01 2014 - 23:45:19 PDT)
- Josh Berryman (Thu May 01 2014 - 23:43:39 PDT)
- Jason Swails (Thu May 01 2014 - 06:15:49 PDT)
- James Starlight (Thu May 01 2014 - 02:05:27 PDT)
[AMBER] Problems with the Amber-14 compilation with CUDA-5.5
- James Starlight (Sat May 03 2014 - 00:10:44 PDT)
- Jason Swails (Thu May 01 2014 - 07:25:57 PDT)
- James Starlight (Thu May 01 2014 - 07:19:30 PDT)
- James Starlight (Thu May 01 2014 - 07:17:15 PDT)
- Daniel Roe (Thu May 01 2014 - 07:15:39 PDT)
- James Starlight (Thu May 01 2014 - 07:06:05 PDT)
- David A Case (Thu May 01 2014 - 06:54:42 PDT)
- James Starlight (Thu May 01 2014 - 06:47:32 PDT)
- David A Case (Thu May 01 2014 - 05:52:15 PDT)
- James Starlight (Thu May 01 2014 - 00:03:22 PDT)
[AMBER] Processing a subset of mdcrd frames
- Daniel Roe (Tue May 06 2014 - 20:29:20 PDT)
- Eugene Yedvabny (Tue May 06 2014 - 15:19:21 PDT)
- Daniel Roe (Tue May 06 2014 - 13:54:15 PDT)
- Eugene Yedvabny (Tue May 06 2014 - 13:34:19 PDT)
[AMBER] Protocol for multiple CPU+ single GPU run on a single node,
- David A Case (Wed May 14 2014 - 13:13:19 PDT)
- Ross Walker (Wed May 14 2014 - 12:49:10 PDT)
- MURAT OZTURK (Wed May 14 2014 - 12:41:37 PDT)
- Ross Walker (Wed May 14 2014 - 12:36:11 PDT)
- Jason Swails (Wed May 14 2014 - 12:33:13 PDT)
- James Maier (Wed May 14 2014 - 12:30:08 PDT)
- MURAT OZTURK (Wed May 14 2014 - 12:22:24 PDT)
- Ross Walker (Wed May 14 2014 - 11:49:41 PDT)
- MURAT OZTURK (Wed May 14 2014 - 11:35:26 PDT)
- Scott Le Grand (Wed May 14 2014 - 11:10:13 PDT)
- Ross Walker (Wed May 14 2014 - 10:39:22 PDT)
- Jason Swails (Wed May 14 2014 - 10:34:53 PDT)
- MURAT OZTURK (Wed May 14 2014 - 10:13:25 PDT)
- Ross Walker (Wed May 14 2014 - 08:57:33 PDT)
- Jason Swails (Wed May 14 2014 - 08:17:32 PDT)
- MURAT OZTURK (Wed May 14 2014 - 07:49:16 PDT)
[AMBER] protonate question
- 王珍 (Sat May 31 2014 - 00:52:15 PDT)
- Jason Swails (Fri May 30 2014 - 06:30:13 PDT)
- 王珍 (Thu May 29 2014 - 17:45:24 PDT)
[AMBER] psf generation
- Jason Swails (Mon May 05 2014 - 03:06:13 PDT)
- Soumendranath Bhakat (Mon May 05 2014 - 01:58:27 PDT)
- sammia khatak (Mon May 05 2014 - 01:44:42 PDT)
[AMBER] QM/MM based binding free energy analysis AMBER
- Soumendranath Bhakat (Mon May 19 2014 - 03:23:09 PDT)
- Nitin Sharma (Mon May 19 2014 - 02:53:24 PDT)
- Soumendranath Bhakat (Sun May 18 2014 - 13:28:46 PDT)
- Nitin Sharma (Sun May 18 2014 - 13:00:26 PDT)
- Soumendranath Bhakat (Sun May 18 2014 - 12:48:28 PDT)
- Nitin Sharma (Sun May 18 2014 - 12:38:26 PDT)
- Soumendranath Bhakat (Sun May 18 2014 - 12:29:58 PDT)
[AMBER] QM/MM tutorial
- Soumendranath Bhakat (Thu May 22 2014 - 07:09:32 PDT)
- Ross Walker (Thu May 22 2014 - 06:49:52 PDT)
- Jason Swails (Thu May 22 2014 - 06:50:24 PDT)
- Soumendranath Bhakat (Thu May 22 2014 - 05:49:38 PDT)
- James Starlight (Thu May 22 2014 - 05:42:28 PDT)
- Jason Swails (Thu May 22 2014 - 05:34:35 PDT)
- James Starlight (Thu May 22 2014 - 05:10:59 PDT)
- Jason Swails (Thu May 22 2014 - 04:29:19 PDT)
- James Starlight (Thu May 22 2014 - 03:27:02 PDT)
- Marc van der Kamp (Mon May 19 2014 - 05:06:56 PDT)
- James Starlight (Sun May 18 2014 - 03:49:47 PDT)
- Marc van der Kamp (Fri May 16 2014 - 04:18:03 PDT)
- James Starlight (Fri May 16 2014 - 03:45:20 PDT)
- James Starlight (Fri May 16 2014 - 03:39:50 PDT)
- Marc van der Kamp (Fri May 16 2014 - 03:33:28 PDT)
- James Starlight (Fri May 16 2014 - 03:05:30 PDT)
- James Starlight (Fri May 16 2014 - 00:26:15 PDT)
- James Starlight (Thu May 15 2014 - 04:06:36 PDT)
- Jason Swails (Thu May 15 2014 - 04:00:11 PDT)
- James Starlight (Thu May 15 2014 - 02:33:28 PDT)
- Daniel Roe (Wed May 14 2014 - 09:42:56 PDT)
- James Starlight (Wed May 14 2014 - 08:55:33 PDT)
- James Starlight (Wed May 14 2014 - 08:20:44 PDT)
- Jason Swails (Wed May 14 2014 - 05:12:17 PDT)
- Marc van der Kamp (Wed May 14 2014 - 05:00:00 PDT)
- Jason Swails (Wed May 14 2014 - 04:29:32 PDT)
- James Starlight (Wed May 14 2014 - 04:00:12 PDT)
- James Starlight (Wed May 14 2014 - 03:15:10 PDT)
- Mark Williamson (Wed May 14 2014 - 02:12:43 PDT)
- James Starlight (Wed May 14 2014 - 01:44:08 PDT)
- Marc van der Kamp (Tue May 13 2014 - 07:06:03 PDT)
- James Starlight (Tue May 13 2014 - 06:09:04 PDT)
- Marc van der Kamp (Tue May 13 2014 - 05:42:52 PDT)
- James Starlight (Tue May 13 2014 - 05:02:46 PDT)
- Marc van der Kamp (Tue May 13 2014 - 04:39:28 PDT)
- James Starlight (Tue May 13 2014 - 04:34:54 PDT)
- Jason Swails (Mon May 12 2014 - 04:13:33 PDT)
- James Starlight (Mon May 12 2014 - 02:32:14 PDT)
[AMBER] Query regarding Amber Advance Tutorial 17
- Kshatresh Dutta Dubey (Thu May 29 2014 - 06:54:23 PDT)
- Jason Swails (Thu May 29 2014 - 05:01:17 PDT)
- Kshatresh Dutta Dubey (Thu May 29 2014 - 01:54:51 PDT)
[AMBER] Question about structure factor?
- David A Case (Wed May 07 2014 - 15:18:20 PDT)
- Xiaoquan Sun (Wed May 07 2014 - 13:33:53 PDT)
[AMBER] Questions about nmode Command
- David A Case (Sun May 04 2014 - 08:25:22 PDT)
- 张明焜 (Sun May 04 2014 - 00:59:01 PDT)
[AMBER] re-imaging bilayer
- Daniel Roe (Wed May 07 2014 - 07:45:45 PDT)
- Jason Swails (Wed May 07 2014 - 05:36:41 PDT)
- Vijay Manickam Achari (Wed May 07 2014 - 05:00:14 PDT)
[AMBER] Recompile amber12 whit cuda 6.0
- Hector A. Baldoni (Mon May 12 2014 - 12:46:15 PDT)
- Ross Walker (Mon May 12 2014 - 12:17:24 PDT)
- Jason Swails (Mon May 12 2014 - 12:18:17 PDT)
- Hector A. Baldoni (Mon May 12 2014 - 12:00:36 PDT)
[AMBER] Regarding Calculation of Hydrogen Bond Energy
- Jason Swails (Thu May 08 2014 - 11:42:20 PDT)
- MOHD HOMAIDUR RAHMAN (Thu May 08 2014 - 11:00:50 PDT)
- MOHD HOMAIDUR RAHMAN (Mon May 05 2014 - 23:30:05 PDT)
[AMBER] REMD velocity information
- Jason Swails (Tue May 13 2014 - 06:06:24 PDT)
- Saikat Dutta Chowdhury (Tue May 13 2014 - 05:05:08 PDT)
[AMBER] request for help in plotting distance matrix plot
- Jason Swails (Sat May 31 2014 - 08:00:17 PDT)
- Soumendranath Bhakat (Fri May 30 2014 - 23:29:24 PDT)
- Robin Jain (Fri May 30 2014 - 23:10:22 PDT)
[AMBER] Residue Pairing ih MMPBSA calculation
- Soumendranath Bhakat (Tue May 27 2014 - 04:15:53 PDT)
- Soumendranath Bhakat (Tue May 27 2014 - 04:13:43 PDT)
- Jason Swails (Tue May 27 2014 - 03:21:57 PDT)
- Arunima Shilpi (Mon May 26 2014 - 20:52:57 PDT)
[AMBER] rmsd of multiple trajectories with different topologies and sizes but same reference
- Brian Radak (Tue May 27 2014 - 08:41:24 PDT)
- Daniel Roe (Tue May 27 2014 - 08:20:55 PDT)
- Brian Radak (Tue May 27 2014 - 07:43:08 PDT)
[AMBER] sander and processor
- Jason Swails (Thu May 15 2014 - 08:38:05 PDT)
- Daniel Roe (Thu May 15 2014 - 08:27:14 PDT)
- sammia khatak (Thu May 15 2014 - 07:09:14 PDT)
[AMBER] sander QM/MM with terachem using MPI
- Daniel Hollas (Sat May 31 2014 - 08:21:42 PDT)
[AMBER] sander restart
- Soumendranath Bhakat (Mon May 19 2014 - 03:18:41 PDT)
- sammia khatak (Mon May 19 2014 - 02:55:22 PDT)
- Soumendranath Bhakat (Mon May 19 2014 - 02:35:10 PDT)
- sammia khatak (Mon May 19 2014 - 02:25:09 PDT)
- Soumendranath Bhakat (Mon May 19 2014 - 00:28:58 PDT)
- sammia khatak (Sun May 18 2014 - 23:57:15 PDT)
[AMBER] sander?
- David A Case (Sun May 04 2014 - 08:27:33 PDT)
- sammia khatak (Sat May 03 2014 - 23:37:16 PDT)
[AMBER] SASA calculation
- Asaminew Haile (Fri May 23 2014 - 06:18:42 PDT)
- Soumendranath Bhakat (Fri May 23 2014 - 06:14:07 PDT)
- Soumendranath Bhakat (Fri May 23 2014 - 05:29:38 PDT)
- Jason Swails (Fri May 23 2014 - 05:16:42 PDT)
- Soumendranath Bhakat (Fri May 23 2014 - 05:07:53 PDT)
[AMBER] SASA error
- Soumendranath Bhakat (Fri May 23 2014 - 08:29:07 PDT)
- Asaminew Haile (Fri May 23 2014 - 08:19:03 PDT)
- Soumendranath Bhakat (Fri May 23 2014 - 06:31:13 PDT)
[AMBER] Saturday
- Bill Ross (Fri May 16 2014 - 13:08:11 PDT)
[AMBER] Scaling of atomic mass of water molecules
- Manikanthan Bhavaraju (Tue May 13 2014 - 10:45:47 PDT)
- Sergio R Aragon (Tue May 13 2014 - 10:35:18 PDT)
- Manikanthan Bhavaraju (Tue May 13 2014 - 10:05:22 PDT)
- Adrian Roitberg (Tue May 13 2014 - 09:50:20 PDT)
- Manikanthan Bhavaraju (Tue May 13 2014 - 08:37:55 PDT)
- Carlos Simmerling (Tue May 13 2014 - 08:31:26 PDT)
- Manikanthan Bhavaraju (Tue May 13 2014 - 08:26:26 PDT)
- Brian Radak (Tue May 13 2014 - 08:21:58 PDT)
- Manikanthan Bhavaraju (Tue May 13 2014 - 08:16:41 PDT)
- Brian Radak (Tue May 13 2014 - 07:59:59 PDT)
- Manikanthan Bhavaraju (Tue May 13 2014 - 07:51:44 PDT)
[AMBER] Script for Calculating RMSIP
- Yip Yew Mun (Tue May 20 2014 - 19:33:20 PDT)
- Daniel Roe (Mon May 19 2014 - 07:10:35 PDT)
- Hector A. Baldoni (Sat May 17 2014 - 16:31:52 PDT)
- Yip Yew Mun (Sat May 17 2014 - 08:54:30 PDT)
[AMBER] secondary structure calculation using Cpptraj
- Marlet Martinez (Wed May 21 2014 - 00:30:54 PDT)
- Daniel Roe (Tue May 20 2014 - 13:45:41 PDT)
- Marlet Martinez (Tue May 20 2014 - 13:00:20 PDT)
[AMBER] Secondary Structure Script
- Soumendranath Bhakat (Fri May 23 2014 - 03:45:42 PDT)
[AMBER] Siginificance of delta G
- Jason Swails (Fri May 09 2014 - 06:36:52 PDT)
- Arunima Shilpi (Fri May 09 2014 - 06:09:27 PDT)
[AMBER] Simulation of the protein with internal water
- James Starlight (Wed May 21 2014 - 05:39:02 PDT)
[AMBER] Simulations using pmemd.cuda
- James Starlight (Wed May 07 2014 - 23:36:06 PDT)
- Ross Walker (Wed May 07 2014 - 08:44:36 PDT)
- Jason Swails (Wed May 07 2014 - 04:34:15 PDT)
- James Starlight (Wed May 07 2014 - 03:39:12 PDT)
- James Starlight (Wed May 07 2014 - 03:18:00 PDT)
- Marc van der Kamp (Wed May 07 2014 - 03:10:34 PDT)
- James Starlight (Wed May 07 2014 - 02:31:53 PDT)
[AMBER] softcore potential flag
- Brian Radak (Thu May 08 2014 - 10:17:58 PDT)
- Asaminew Haile (Thu May 08 2014 - 09:44:04 PDT)
- David A Case (Thu May 08 2014 - 09:32:33 PDT)
- Asaminew Haile (Thu May 08 2014 - 07:37:23 PDT)
[AMBER] SolvateBox command
- Bill Ross (Thu May 15 2014 - 16:30:00 PDT)
- George Patargias (Thu May 08 2014 - 08:13:35 PDT)
- Jason Swails (Thu May 08 2014 - 04:25:42 PDT)
- George Patargias (Thu May 08 2014 - 03:50:34 PDT)
[AMBER] solvating molecule
- kirtana S (Thu May 01 2014 - 18:26:36 PDT)
[AMBER] sqm convergence failure
- FyD (Tue May 20 2014 - 13:30:38 PDT)
- Jason Swails (Tue May 20 2014 - 09:00:02 PDT)
- David A Case (Tue May 20 2014 - 08:30:20 PDT)
- Gerald Monard (Tue May 20 2014 - 07:57:04 PDT)
- David A Case (Mon May 12 2014 - 05:01:22 PDT)
- Jason Swails (Mon May 12 2014 - 04:10:35 PDT)
- Hannes Loeffler (Mon May 12 2014 - 02:54:48 PDT)
- David A Case (Fri May 09 2014 - 12:49:27 PDT)
- hannes.loeffler.stfc.ac.uk (Thu May 08 2014 - 10:44:41 PDT)
- Jason Swails (Thu May 08 2014 - 06:25:02 PDT)
- Hannes Loeffler (Thu May 08 2014 - 05:49:09 PDT)
- Jason Swails (Thu May 08 2014 - 05:22:41 PDT)
- Hannes Loeffler (Thu May 08 2014 - 05:03:56 PDT)
- FyD (Thu May 08 2014 - 04:23:27 PDT)
- Hannes Loeffler (Thu May 08 2014 - 03:16:06 PDT)
[AMBER] SQM: How to extract the charge density of sqm runs?
- Marc van der Kamp (Tue May 20 2014 - 02:35:26 PDT)
[AMBER] sudden and rapid configuration change in NVT simulation
- Soumendranath Bhakat (Fri May 30 2014 - 02:17:51 PDT)
- yjlee (Fri May 30 2014 - 01:44:46 PDT)
[AMBER] syntax error and nab2c failed when using NAB
- Jason Swails (Thu May 08 2014 - 06:41:20 PDT)
- Dongshan Wei (Thu May 08 2014 - 06:27:15 PDT)
- Dongshan Wei (Thu May 08 2014 - 06:05:30 PDT)
- David A Case (Thu May 08 2014 - 05:59:21 PDT)
- Jason Swails (Thu May 08 2014 - 05:54:43 PDT)
- Dongshan Wei (Thu May 08 2014 - 05:36:37 PDT)
- Jason Swails (Thu May 08 2014 - 05:23:40 PDT)
- Dongshan Wei (Thu May 08 2014 - 05:14:00 PDT)
- Jason Swails (Thu May 08 2014 - 04:56:49 PDT)
- Dongshan Wei (Thu May 08 2014 - 02:23:18 PDT)
[AMBER] Temperature rises to 4000K during NVT equilibration
- Daniel Roe (Wed May 21 2014 - 11:51:13 PDT)
- Indrajit Deb (Wed May 21 2014 - 11:14:20 PDT)
- Jason Swails (Wed May 21 2014 - 08:40:51 PDT)
- Indrajit Deb (Wed May 21 2014 - 07:56:35 PDT)
- David A Case (Wed May 21 2014 - 07:29:57 PDT)
- Daniel Roe (Wed May 21 2014 - 07:14:07 PDT)
- Indrajit Deb (Wed May 21 2014 - 07:07:51 PDT)
- Daniel Roe (Wed May 21 2014 - 07:03:19 PDT)
- Indrajit Deb (Wed May 21 2014 - 06:55:46 PDT)
[AMBER] thermodynamic integration (TI) simulation: pmemd of amber14 vs sander of amber11- vdw transformation
- Ross Walker (Wed May 14 2014 - 08:05:39 PDT)
- Jason Swails (Wed May 14 2014 - 04:37:01 PDT)
- Ying-Chieh Sun (Wed May 14 2014 - 03:21:17 PDT)
[AMBER] Topology and Corresponding PDB Amber
- Jason Swails (Sat May 24 2014 - 13:37:47 PDT)
- Soumendranath Bhakat (Sat May 24 2014 - 12:39:49 PDT)
[AMBER] torsion restraints not defined properly?
- Duggan, Brendan (Tue May 20 2014 - 11:55:30 PDT)
- Daniel Roe (Thu May 15 2014 - 13:43:40 PDT)
- David A Case (Thu May 15 2014 - 12:12:52 PDT)
- Daniel Roe (Thu May 15 2014 - 11:05:53 PDT)
- Duggan, Brendan (Thu May 15 2014 - 10:55:29 PDT)
[AMBER] Trajectory analysis using pptraj
- Daniel Roe (Tue May 27 2014 - 06:37:18 PDT)
- James Starlight (Sun May 25 2014 - 03:50:01 PDT)
- Jason Swails (Thu May 22 2014 - 06:22:44 PDT)
- James Starlight (Thu May 22 2014 - 05:52:19 PDT)
- Jason Swails (Wed May 21 2014 - 08:38:27 PDT)
- Vlad Cojocaru (Wed May 21 2014 - 08:24:17 PDT)
- James Starlight (Wed May 21 2014 - 08:19:42 PDT)
- Daniel Roe (Tue May 20 2014 - 08:57:29 PDT)
- James Starlight (Tue May 20 2014 - 08:05:38 PDT)
[AMBER] Unit cell vectors are NOT rotated; imaging will not be possible
- newamber list (Sat May 17 2014 - 11:09:56 PDT)
- Jason Swails (Sat May 17 2014 - 10:49:45 PDT)
- newamber list (Sat May 17 2014 - 09:41:38 PDT)
[AMBER] Urgent: unable to generate files
- Jason Swails (Tue May 13 2014 - 04:37:30 PDT)
- liu junjun (Tue May 13 2014 - 03:49:36 PDT)
- Faez Iqbal khan (Tue May 13 2014 - 01:20:43 PDT)
[AMBER] valve of VDW too high
- Jason Swails (Thu May 08 2014 - 04:41:34 PDT)
- David Chen (Thu May 08 2014 - 04:28:25 PDT)
[AMBER] vlimit exceeded error when switch from NPT to NVE
- Quynh Vo (Sun May 04 2014 - 11:06:42 PDT)
- David A Case (Sun May 04 2014 - 04:46:46 PDT)
- Quynh Vo (Sat May 03 2014 - 22:39:22 PDT)
[AMBER] when nastruct does NOT print the basepair information
- Daniel Roe (Thu May 15 2014 - 08:25:38 PDT)
- newamber list (Thu May 15 2014 - 07:52:04 PDT)
[AMBER] z-axis restraints
- Pierpaolo Cacciotto (Thu May 22 2014 - 06:49:37 PDT)
[AMBER] zinc partial charges
- FyD (Wed May 28 2014 - 23:57:42 PDT)
- Nash, Anthony (Tue May 27 2014 - 23:30:38 PDT)
[AMBER] 答复: About the reproducibility of pmemd
- Jason Swails (Tue May 20 2014 - 06:30:29 PDT)
- Val Yu (Tue May 20 2014 - 05:56:53 PDT)
[q4md-fft] FAD parameters from F-90
- FyD (Sun May 04 2014 - 22:02:54 PDT)
Amber webminar
- Adrian Roitberg (Tue May 06 2014 - 11:55:07 PDT)
in vacuo dynamics)
- Scott Le Grand (Tue May 27 2014 - 20:57:03 PDT)
- Jason Swails (Tue May 27 2014 - 19:14:38 PDT)
- Robert McGibbon (Tue May 27 2014 - 14:11:41 PDT)
- Scott Le Grand (Tue May 27 2014 - 12:21:18 PDT)
- Jason Swails (Mon May 26 2014 - 15:35:44 PDT)
PDB for 1-octanol molecules
- FyD (Wed May 07 2014 - 08:16:17 PDT)
thermodynamic integration (TI) simulation: pmemd of amber14 vs sander of amber11- vdw transformation
- Ross Walker (Wed May 14 2014 - 21:16:29 PDT)
- Ying-Chieh Sun (Wed May 14 2014 - 20:42:24 PDT)

Amber Archive May 2014 by subject