Amber Archive Aug 2016: by subject

[AMBER] (no subject)
- Jason Swails (Mon Aug 29 2016 - 08:27:33 PDT)
- Hai Nguyen (Sat Aug 27 2016 - 20:34:02 PDT)
- Amrullah13 (Sat Aug 27 2016 - 18:51:50 PDT)
[AMBER] 180 degrees of angle in AMBER 10
- Jason Swails (Thu Aug 04 2016 - 13:30:36 PDT)
- Pengzhi Zhang (Wed Aug 03 2016 - 13:07:26 PDT)
[AMBER] 22.1.6.1. Free Energy using linear scaling 22.1.6.2.Absolute free energy using soft core,
- Hannes Loeffler (Wed Aug 24 2016 - 04:58:58 PDT)
- Markus Kaukonen (Wed Aug 24 2016 - 01:01:45 PDT)
[AMBER] 3 trajectory MMPBSA free energy calculation
- JoAnne Babula (Wed Aug 10 2016 - 11:04:44 PDT)
- Amy Rice (Wed Aug 10 2016 - 08:34:15 PDT)
- JoAnne Babula (Wed Aug 10 2016 - 07:47:45 PDT)
[AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan
- Bill Ross (Sat Aug 27 2016 - 15:33:52 PDT)
- mirko hennig (Sat Aug 27 2016 - 15:32:25 PDT)
- Nhai (Sat Aug 27 2016 - 15:07:14 PDT)
- mirko hennig (Sat Aug 27 2016 - 09:52:04 PDT)
- Jason Swails (Fri Aug 19 2016 - 05:51:35 PDT)
- Jason Swails (Thu Aug 18 2016 - 05:18:47 PDT)
- mirko hennig (Tue Aug 16 2016 - 07:53:42 PDT)
- David A Case (Tue Aug 16 2016 - 04:57:21 PDT)
- mirko hennig (Tue Aug 16 2016 - 00:18:10 PDT)
- Jason Swails (Mon Aug 15 2016 - 18:56:04 PDT)
- David A Case (Mon Aug 15 2016 - 13:32:38 PDT)
- mirko hennig (Mon Aug 15 2016 - 11:00:40 PDT)
- Hai Nguyen (Mon Aug 15 2016 - 10:15:04 PDT)
- mirko hennig (Mon Aug 15 2016 - 10:03:04 PDT)
- David A Case (Mon Aug 15 2016 - 10:00:30 PDT)
- Hai Nguyen (Mon Aug 15 2016 - 09:50:41 PDT)
- mirko hennig (Mon Aug 15 2016 - 09:26:56 PDT)
[AMBER] a bug in leaprc.gaff2 file
- David A Case (Thu Aug 18 2016 - 11:07:07 PDT)
- David A Case (Thu Aug 18 2016 - 06:22:25 PDT)
- Ye Mei (Thu Aug 18 2016 - 02:21:16 PDT)
[AMBER] about lipids retrain
- Albert (Wed Aug 17 2016 - 05:26:59 PDT)
- David A Case (Wed Aug 17 2016 - 04:48:00 PDT)
- Albert (Wed Aug 17 2016 - 02:45:19 PDT)
[AMBER] Accelerated MD -- cudaMemcpy error
- Daniel Roe (Tue Aug 16 2016 - 07:58:59 PDT)
- DmitryASuplatov (Tue Aug 16 2016 - 04:05:38 PDT)
- Daniel Roe (Mon Aug 15 2016 - 11:01:27 PDT)
- DmitryASuplatov (Mon Aug 15 2016 - 03:52:14 PDT)
- Dmitry Suplatov (Fri Aug 12 2016 - 13:53:07 PDT)
[AMBER] Adaptively Biased MD Simulations of type "distance" using "FLOODING"
- Feng Pan (Mon Aug 22 2016 - 08:25:24 PDT)
- Bill Ross (Mon Aug 22 2016 - 03:54:06 PDT)
- Bill Ross (Mon Aug 22 2016 - 03:45:53 PDT)
- Emmanuel (Mon Aug 22 2016 - 03:32:05 PDT)
[AMBER] Alanine scan of nonnatural amino acid
- Jason Swails (Tue Aug 23 2016 - 09:21:07 PDT)
- Aronica, Pietro (Tue Aug 23 2016 - 02:21:37 PDT)
[AMBER] Amber 14.13 pmemd.cuda: Error: invalid configuration argument launching kernel kPMEReduceChargeGridBuffer
- William Lees (Fri Aug 12 2016 - 06:19:05 PDT)
- Ross Walker (Wed Aug 10 2016 - 20:01:52 PDT)
- William Lees (Wed Aug 10 2016 - 02:02:59 PDT)
[AMBER] Amber B5 tutorial
- David A Case (Fri Aug 12 2016 - 12:22:25 PDT)
- Chitrak Gupta (Fri Aug 12 2016 - 11:10:05 PDT)
[AMBER] Amber Force Fields
- Carlos Simmerling (Wed Aug 31 2016 - 17:34:12 PDT)
- Hai Nguyen (Wed Aug 31 2016 - 12:40:45 PDT)
- amir sadeghi (Wed Aug 31 2016 - 12:33:48 PDT)
[AMBER] amber pdb > 100,000 atoms
- David A Case (Fri Aug 12 2016 - 05:42:19 PDT)
- Marc van der Kamp (Fri Aug 12 2016 - 01:19:18 PDT)
- Neha Gandhi (Fri Aug 12 2016 - 00:53:28 PDT)
[AMBER] Amber14 FEW for 3 trajectory free energy
- JoAnne Babula (Tue Aug 09 2016 - 11:02:24 PDT)
- Amy Rice (Fri Aug 05 2016 - 08:21:50 PDT)
- JoAnne Babula (Fri Aug 05 2016 - 07:32:22 PDT)
[AMBER] Amber16 installation error.
- Abhilash J (Thu Aug 11 2016 - 14:19:11 PDT)
- Hai Nguyen (Thu Aug 11 2016 - 14:06:31 PDT)
- Abhilash J (Thu Aug 11 2016 - 14:00:32 PDT)
- Abhilash J (Thu Aug 11 2016 - 13:44:56 PDT)
- Hai Nguyen (Thu Aug 11 2016 - 13:36:56 PDT)
- Abhilash J (Thu Aug 11 2016 - 13:27:52 PDT)
- Hai Nguyen (Thu Aug 11 2016 - 13:16:30 PDT)
- Hai Nguyen (Thu Aug 11 2016 - 13:13:53 PDT)
- Abhilash J (Thu Aug 11 2016 - 13:04:45 PDT)
- Hai Nguyen (Thu Aug 11 2016 - 12:52:46 PDT)
- Abhilash J (Thu Aug 11 2016 - 12:45:35 PDT)
- Hai Nguyen (Thu Aug 11 2016 - 12:41:34 PDT)
- Abhilash J (Thu Aug 11 2016 - 12:18:33 PDT)
- Hai Nguyen (Thu Aug 11 2016 - 12:12:35 PDT)
- Abhilash J (Thu Aug 11 2016 - 12:06:33 PDT)
- Hai Nguyen (Thu Aug 11 2016 - 11:54:41 PDT)
- Abhilash J (Thu Aug 11 2016 - 07:55:00 PDT)
[AMBER] Amber16 Parallel CUDA Tests
- Steven Ford (Fri Aug 12 2016 - 09:44:54 PDT)
- Ross Walker (Thu Aug 11 2016 - 21:39:19 PDT)
- Steven Ford (Thu Aug 11 2016 - 21:38:10 PDT)
- Steven Ford (Thu Aug 11 2016 - 21:33:15 PDT)
- Ross Walker (Thu Aug 11 2016 - 21:29:05 PDT)
- Steven Ford (Thu Aug 11 2016 - 21:21:52 PDT)
- Ross Walker (Thu Aug 11 2016 - 20:17:16 PDT)
- Steven Ford (Thu Aug 11 2016 - 19:54:15 PDT)
[AMBER] amber16/test/qmmm_DFTB
- Dr. Andreas W. Goetz (Thu Aug 04 2016 - 23:27:47 PDT)
- Markus Kaukonen (Thu Aug 04 2016 - 23:13:12 PDT)
[AMBER] Amber´14 Solvent box simulation, something went wrong!!
- Daniel Roe (Thu Aug 04 2016 - 08:02:28 PDT)
- Stregone (Thu Aug 04 2016 - 02:08:37 PDT)
- Daniel Roe (Wed Aug 03 2016 - 12:30:45 PDT)
- Stregone (Wed Aug 03 2016 - 06:43:18 PDT)
[AMBER] antechamber cannot match patching atoms of amino acid
- FyD (Fri Aug 12 2016 - 01:12:01 PDT)
- David A Case (Thu Aug 11 2016 - 05:05:53 PDT)
- Chitrak Gupta (Wed Aug 10 2016 - 15:26:24 PDT)
[AMBER] autocorr of hydrogen bonds
- Osman, Roman (Tue Aug 30 2016 - 14:41:38 PDT)
- Tom Kurtzman (Tue Aug 30 2016 - 08:07:36 PDT)
- Osman, Roman (Mon Aug 29 2016 - 06:05:06 PDT)
[AMBER] autoimage bug?
- Daniel Roe (Wed Aug 31 2016 - 06:22:55 PDT)
- Filip Persson (Mon Aug 29 2016 - 05:36:24 PDT)
[AMBER] begin time read from input coords
- Hannes Loeffler (Fri Aug 26 2016 - 08:34:45 PDT)
- David A Case (Fri Aug 26 2016 - 06:11:04 PDT)
- Hannes Loeffler (Fri Aug 26 2016 - 05:01:40 PDT)
- Daniel Roe (Fri Aug 26 2016 - 03:17:33 PDT)
- Hannes Loeffler (Fri Aug 26 2016 - 01:10:09 PDT)
[AMBER] bellymask option.
- Saman Yousuf ali (Tue Aug 16 2016 - 07:48:26 PDT)
- David A Case (Tue Aug 16 2016 - 04:59:16 PDT)
- Saman Yousuf ali (Mon Aug 15 2016 - 19:24:05 PDT)
[AMBER] box of polar molecules using amoeba force field
- Xiaoliu Zhang (Fri Aug 05 2016 - 14:32:46 PDT)
[AMBER] Calculating lipid diffusion using stfcdiffusion
- Amy Rice (Mon Aug 01 2016 - 12:35:03 PDT)
- Daniel Roe (Mon Aug 01 2016 - 12:24:37 PDT)
- Amy Rice (Mon Aug 01 2016 - 12:06:53 PDT)
[AMBER] Calculating Salt bridge interactions- Protein and RNA
- Daniel Roe (Mon Aug 01 2016 - 10:26:14 PDT)
[AMBER] change the atom charge in a restart simulations
- David A Case (Wed Aug 31 2016 - 05:32:25 PDT)
- Bill Ross (Wed Aug 31 2016 - 02:54:44 PDT)
- windy (Wed Aug 31 2016 - 01:49:25 PDT)
[AMBER] changing atom type
- Dr. Andreas W. Goetz (Wed Aug 31 2016 - 14:15:35 PDT)
- Jason Swails (Wed Aug 31 2016 - 09:00:20 PDT)
- Hai Nguyen (Wed Aug 31 2016 - 08:41:22 PDT)
- Jacopo Sgrignani (Wed Aug 31 2016 - 08:16:37 PDT)
[AMBER] CHARM force field
- Jason Swails (Mon Aug 15 2016 - 18:50:22 PDT)
- Chi Jin (Mon Aug 15 2016 - 13:48:12 PDT)
[AMBER] Checking AmberTools16 installation
- Hai Nguyen (Tue Aug 30 2016 - 10:07:17 PDT)
- Hai Nguyen (Tue Aug 30 2016 - 09:30:49 PDT)
- Bence Hégely (Tue Aug 30 2016 - 07:37:58 PDT)
- Hai Nguyen (Mon Aug 29 2016 - 10:09:08 PDT)
- Bence Hégely (Fri Aug 26 2016 - 07:19:10 PDT)
- Hai Nguyen (Thu Aug 25 2016 - 12:45:01 PDT)
- Bence Hégely (Thu Aug 25 2016 - 11:53:11 PDT)
[AMBER] Checking modeling after MCPB and unable to fix atom order using cpptraj
- Andrew Schaub (Tue Aug 23 2016 - 22:56:02 PDT)
- Hai Nguyen (Tue Aug 23 2016 - 22:44:43 PDT)
- Andrew Schaub (Tue Aug 23 2016 - 22:15:58 PDT)
[AMBER] Combining single structure NMR pdb files into an ensemble.
- Erik Davis (Wed Aug 17 2016 - 06:05:24 PDT)
- Hai Nguyen (Tue Aug 16 2016 - 13:45:14 PDT)
- Erik Davis (Tue Aug 16 2016 - 13:38:05 PDT)
[AMBER] concerns on membrane protein restrain
- Albert (Fri Aug 19 2016 - 11:39:35 PDT)
[AMBER] Converting rst to pdb
- Corum, Katharine W (Tue Aug 09 2016 - 16:26:09 PDT)
- Daniel Roe (Tue Aug 09 2016 - 14:22:17 PDT)
- Hai Nguyen (Tue Aug 09 2016 - 14:09:46 PDT)
- Corum, Katharine W (Tue Aug 09 2016 - 14:01:58 PDT)
[AMBER] Copper +1 and membrane with LJ 12-6-4 potential
- Pengfei Li (Sat Aug 27 2016 - 13:48:22 PDT)
- Stephan Schott (Tue Aug 23 2016 - 07:37:52 PDT)
[AMBER] copy charges using Python API
- William Lees (Tue Aug 09 2016 - 02:07:50 PDT)
- Hai Nguyen (Mon Aug 08 2016 - 12:06:07 PDT)
- David A Case (Mon Aug 08 2016 - 05:16:13 PDT)
- Thomas Evangelidis (Mon Aug 08 2016 - 03:00:44 PDT)
- David A Case (Sun Aug 07 2016 - 09:13:06 PDT)
- Thomas Evangelidis (Sun Aug 07 2016 - 06:50:23 PDT)
- Jason Swails (Sun Aug 07 2016 - 06:05:35 PDT)
- Thomas Evangelidis (Sun Aug 07 2016 - 04:28:38 PDT)
[AMBER] correlated dihedral force constant
- Chi Jin (Tue Aug 02 2016 - 12:46:23 PDT)
[AMBER] cpptraj issues
- Daniel Roe (Fri Aug 12 2016 - 10:56:20 PDT)
- Thomas Pochapsky (Fri Aug 12 2016 - 09:52:19 PDT)
[AMBER] cpptraj on pH-REMD
- Jason Swails (Wed Aug 24 2016 - 19:34:16 PDT)
- Elisa Pieri (Wed Aug 24 2016 - 04:19:10 PDT)
[AMBER] Cpptraj-PCA Warning
- Ilkow, Veronica (Fri Aug 05 2016 - 07:15:50 PDT)
[AMBER] Cyana3.97 to Amber15 pdb conversion
- Erik Davis (Fri Aug 05 2016 - 11:01:46 PDT)
- David A Case (Wed Aug 03 2016 - 16:41:13 PDT)
- Daniel Roe (Wed Aug 03 2016 - 12:26:52 PDT)
- Erik Davis (Wed Aug 03 2016 - 08:09:35 PDT)
[AMBER] default value (inp= 0,1,2)? MMPBSA
- Ray Luo (Mon Aug 01 2016 - 12:25:42 PDT)
- Thakur, Abhishek (Mon Aug 01 2016 - 11:42:29 PDT)
- Ray Luo (Mon Aug 01 2016 - 10:35:04 PDT)
- Thakur, Abhishek (Mon Aug 01 2016 - 09:35:16 PDT)
[AMBER] Difference of two trajectories
- Daniel Roe (Mon Aug 01 2016 - 10:27:33 PDT)
[AMBER] does AMBER already have Pt parameters for modeling cisplatin like compounds?
- Pengfei Li (Wed Aug 10 2016 - 06:37:06 PDT)
- Vaibhav Dixit (Wed Aug 10 2016 - 04:49:05 PDT)
[AMBER] Does Scaled MD require NVT ensemble?
- Harshavardhan Khare (Fri Aug 19 2016 - 22:01:53 PDT)
- Ross Walker (Fri Aug 19 2016 - 07:13:12 PDT)
- Harshavardhan Khare (Thu Aug 18 2016 - 23:20:40 PDT)
[AMBER] EEL become ****** in minimization
- David A Case (Mon Aug 01 2016 - 08:04:15 PDT)
- David Cerutti (Sun Jul 31 2016 - 22:04:36 PDT)
- Suguru ASAI (Sun Jul 31 2016 - 21:10:44 PDT)
[AMBER] EEL energy of QM/MM-GBSA
- David A Case (Mon Aug 01 2016 - 07:58:39 PDT)
- 张姝姝 (Sun Jul 31 2016 - 20:11:42 PDT)
[AMBER] EM in vacuum
- David A Case (Wed Aug 03 2016 - 16:22:18 PDT)
- Dmitry Suplatov (Tue Aug 02 2016 - 13:52:17 PDT)
[AMBER] Energy overflow in MD with distance restraint under PBC (aMD problem?)
- Daniel Roe (Tue Aug 02 2016 - 08:25:42 PDT)
- Stephan Schott (Tue Aug 02 2016 - 07:00:29 PDT)
[AMBER] error in mdcrd box coordinates during MMPBSA calculation
- Jason Swails (Tue Aug 23 2016 - 09:25:45 PDT)
- JoAnne Babula (Mon Aug 22 2016 - 17:56:23 PDT)
- Hai Nguyen (Mon Aug 22 2016 - 10:17:51 PDT)
- JoAnne Babula (Mon Aug 22 2016 - 09:58:21 PDT)
- Hai Nguyen (Mon Aug 22 2016 - 09:40:38 PDT)
- JoAnne Babula (Mon Aug 22 2016 - 09:04:27 PDT)
- JoAnne Babula (Mon Aug 22 2016 - 08:54:16 PDT)
- Nhai (Mon Aug 22 2016 - 08:38:38 PDT)
- JoAnne Babula (Mon Aug 22 2016 - 08:33:56 PDT)
- Nhai (Mon Aug 22 2016 - 08:31:42 PDT)
- JoAnne Babula (Mon Aug 22 2016 - 07:19:03 PDT)
- Bilal Nizami (Sat Aug 13 2016 - 01:11:11 PDT)
- Hai Nguyen (Fri Aug 12 2016 - 11:49:05 PDT)
- JoAnne Babula (Fri Aug 12 2016 - 11:41:21 PDT)
- Amy Rice (Fri Aug 12 2016 - 10:46:30 PDT)
- JoAnne Babula (Fri Aug 12 2016 - 10:38:24 PDT)
- JoAnne Babula (Fri Aug 12 2016 - 10:34:41 PDT)
- Bilal Nizami (Fri Aug 12 2016 - 00:15:01 PDT)
- Hai Nguyen (Thu Aug 11 2016 - 11:49:15 PDT)
- JoAnne Babula (Thu Aug 11 2016 - 11:41:31 PDT)
- Hai Nguyen (Thu Aug 11 2016 - 11:32:25 PDT)
- JoAnne Babula (Thu Aug 11 2016 - 08:21:11 PDT)
[AMBER] error in runing mdout_analyzer.py
- Daniel Roe (Thu Aug 04 2016 - 08:05:51 PDT)
- nida baig (Wed Aug 03 2016 - 21:39:05 PDT)
- Daniel Roe (Wed Aug 03 2016 - 21:25:23 PDT)
- nida baig (Wed Aug 03 2016 - 21:10:04 PDT)
[AMBER] error in sander and sander.mpi running
- Daniel Roe (Tue Aug 16 2016 - 07:52:01 PDT)
- leila karami (Sun Aug 14 2016 - 05:24:31 PDT)
- leila karami (Sun Aug 14 2016 - 04:11:11 PDT)
[AMBER] error running production with restraint.
- Saman Yousuf ali (Sat Aug 06 2016 - 02:29:13 PDT)
- David A Case (Fri Aug 05 2016 - 04:55:29 PDT)
- Saman Yousuf ali (Fri Aug 05 2016 - 02:04:39 PDT)
- zoran matovic (Fri Aug 05 2016 - 00:14:00 PDT)
- zoran matovic (Thu Aug 04 2016 - 11:38:52 PDT)
- zoran matovic (Thu Aug 04 2016 - 11:27:49 PDT)
- Daniel Roe (Thu Aug 04 2016 - 08:04:48 PDT)
- Saman Yousuf ali (Wed Aug 03 2016 - 22:16:51 PDT)
[AMBER] Error with nmode calculations
- Jason Swails (Fri Aug 05 2016 - 12:10:33 PDT)
- Praneeth Bommisetti (Fri Aug 05 2016 - 11:10:32 PDT)
[AMBER] errors in doing TI tutorial calculation
- Hannes Loeffler (Mon Aug 29 2016 - 12:26:33 PDT)
- David A Case (Mon Aug 29 2016 - 12:25:59 PDT)
- 张姝姝 (Mon Aug 29 2016 - 07:26:56 PDT)
[AMBER] EVB calculations of proton transfer
- David A Case (Tue Aug 02 2016 - 07:38:37 PDT)
- kenfack cyril (Mon Aug 01 2016 - 14:05:09 PDT)
- David A Case (Mon Aug 01 2016 - 07:52:43 PDT)
[AMBER] Extend of manual modulation-Connecting two molecules methodology
- Kostas Bourandas (Mon Aug 08 2016 - 19:56:53 PDT)
- David A Case (Sat Aug 06 2016 - 19:27:23 PDT)
- Kostas Bourandas (Sat Aug 06 2016 - 13:32:44 PDT)
[AMBER] File redirection commands with targeted MD
- Sonia Ziada (Wed Aug 31 2016 - 09:10:52 PDT)
[AMBER] for what kind of post simulation analysis I need to do reweighing?
- Christina Bergonzo (Tue Aug 09 2016 - 09:18:41 PDT)
- Thakur, Abhishek (Tue Aug 09 2016 - 08:08:32 PDT)
- Adrian Roitberg (Tue Aug 09 2016 - 08:04:05 PDT)
- Thakur, Abhishek (Tue Aug 09 2016 - 08:01:27 PDT)
[AMBER] Frac in cpptraj hydrogen bond command.
- Daniel Roe (Sun Aug 21 2016 - 05:55:13 PDT)
- Saman Yousuf ali (Sun Aug 21 2016 - 05:25:42 PDT)
[AMBER] frozen geometry setting?
- Michael Shokhen (Wed Aug 31 2016 - 06:34:36 PDT)
- Bill Ross (Tue Aug 30 2016 - 12:32:16 PDT)
- Adrian Roitberg (Tue Aug 30 2016 - 12:14:29 PDT)
- Michael Shokhen (Tue Aug 30 2016 - 12:12:33 PDT)
- Bill Ross (Tue Aug 30 2016 - 11:59:10 PDT)
- Michael Shokhen (Tue Aug 30 2016 - 11:55:56 PDT)
- David A Case (Tue Aug 30 2016 - 08:26:12 PDT)
- Michael Shokhen (Tue Aug 30 2016 - 07:32:09 PDT)
[AMBER] Fwd: cpptraj issues
- Thomas Pochapsky (Tue Aug 16 2016 - 08:23:25 PDT)
- Daniel Roe (Tue Aug 16 2016 - 07:56:01 PDT)
- Thomas Pochapsky (Tue Aug 16 2016 - 07:20:30 PDT)
- Daniel Roe (Mon Aug 15 2016 - 10:45:40 PDT)
- Thomas Pochapsky (Mon Aug 15 2016 - 08:02:22 PDT)
[AMBER] Fwd: Regarding antechamber command Error
- Vishal Nemaysh (Thu Aug 11 2016 - 00:10:40 PDT)
[AMBER] gbsa parameter
- Daniel Roe (Wed Aug 03 2016 - 12:23:03 PDT)
- Hai Nguyen (Wed Aug 03 2016 - 09:33:14 PDT)
- Thomas Evangelidis (Wed Aug 03 2016 - 08:54:11 PDT)
[AMBER] Generate Polymer parameters
- David A Case (Wed Aug 03 2016 - 16:47:17 PDT)
- konda003 . (Wed Aug 03 2016 - 12:58:24 PDT)
[AMBER] Generating parameter and topology files for a protein with multiple Zinc ions
- Pengfei Li (Sat Aug 27 2016 - 13:55:54 PDT)
- Bill Ross (Wed Aug 24 2016 - 21:19:37 PDT)
- Aditya Padhi (Tue Aug 23 2016 - 18:00:15 PDT)
[AMBER] Generating topology and parameter file for a peptide
- Bill Ross (Wed Aug 24 2016 - 00:57:27 PDT)
- Hai Nguyen (Tue Aug 23 2016 - 23:37:14 PDT)
- pratibha sharma (Tue Aug 23 2016 - 23:34:57 PDT)
[AMBER] Getting free energy (difference) from GPU simulations
- Jason Swails (Thu Aug 04 2016 - 11:09:44 PDT)
- yunshi11 . (Wed Aug 03 2016 - 16:18:05 PDT)
[AMBER] GPU MPI failed
- Albert (Thu Aug 11 2016 - 06:20:37 PDT)
- David A Case (Thu Aug 11 2016 - 05:15:16 PDT)
- Albert (Thu Aug 11 2016 - 01:37:52 PDT)
[AMBER] GPU peer support disabled
- Hirdesh Kumar (Thu Aug 11 2016 - 14:11:38 PDT)
- Ross Walker (Thu Aug 11 2016 - 14:01:33 PDT)
- Hirdesh Kumar (Thu Aug 11 2016 - 13:53:22 PDT)
[AMBER] HBond command
- Daniel Roe (Tue Aug 02 2016 - 08:49:18 PDT)
- Sidhu, Khushwant (Dr.) (Tue Aug 02 2016 - 05:50:08 PDT)
[AMBER] How to fix the wall of the water box in amber
- Bill Ross (Sun Aug 07 2016 - 02:01:46 PDT)
- Ming Tang (Sat Aug 06 2016 - 22:34:11 PDT)
- Bill Ross (Sat Aug 06 2016 - 18:59:00 PDT)
- Ming Tang (Sat Aug 06 2016 - 18:17:18 PDT)
[AMBER] hydrogen bond occupancy plot cpptraj
- Daniel Roe (Mon Aug 01 2016 - 10:23:57 PDT)
[AMBER] Implicit solvent in pmemd.cuda
- Ross Walker (Fri Aug 05 2016 - 09:39:36 PDT)
- Carlos Simmerling (Fri Aug 05 2016 - 09:31:42 PDT)
- Hai Nguyen (Fri Aug 05 2016 - 09:05:47 PDT)
- Chitrak Gupta (Fri Aug 05 2016 - 08:54:58 PDT)
[AMBER] intel MPI failed
- Albert (Tue Aug 09 2016 - 06:00:17 PDT)
- David A Case (Tue Aug 09 2016 - 04:55:04 PDT)
- Albert (Mon Aug 08 2016 - 23:12:00 PDT)
- Albert (Mon Aug 08 2016 - 07:39:38 PDT)
- Daniel Roe (Mon Aug 08 2016 - 07:37:26 PDT)
- Albert (Mon Aug 08 2016 - 07:26:47 PDT)
- Daniel Roe (Mon Aug 08 2016 - 07:16:04 PDT)
- Albert (Mon Aug 08 2016 - 06:40:54 PDT)
[AMBER] interaction entropy instead of normal mode analysis
- Jason Swails (Thu Aug 04 2016 - 11:03:44 PDT)
- diaby (Tue Aug 02 2016 - 06:57:10 PDT)
[AMBER] InVacuoWithDielc
- JAIME RUBIO MARTINEZ (Tue Aug 02 2016 - 00:32:58 PDT)
[AMBER] Is there a way to disable electrostatic solute-solvent interactions in PMEMD?
- Jason Swails (Thu Aug 04 2016 - 11:02:00 PDT)
- Plotnikov, Nikolay (Thu Aug 04 2016 - 08:27:25 PDT)
[AMBER] Is there any CG martini parameter for K+?
- Pengfei Li (Wed Aug 17 2016 - 13:40:33 PDT)
- li he (Wed Aug 17 2016 - 11:18:34 PDT)
[AMBER] Issues compiling Amber with CUDA support
- Baker, Joseph (Sat Aug 27 2016 - 21:48:21 PDT)
- Ross Walker (Sat Aug 27 2016 - 15:53:28 PDT)
- Baker, Joseph (Sat Aug 27 2016 - 13:10:31 PDT)
- Ross Walker (Thu Aug 25 2016 - 04:30:46 PDT)
- Sivy, Shawn (Wed Aug 24 2016 - 11:47:10 PDT)
[AMBER] job failed
- David A Case (Sun Aug 14 2016 - 06:03:23 PDT)
- Albert (Sat Aug 13 2016 - 23:37:26 PDT)
[AMBER] job suspended
- Nhai (Fri Aug 12 2016 - 08:26:09 PDT)
- Albert (Fri Aug 12 2016 - 08:15:42 PDT)
- David A Case (Fri Aug 12 2016 - 08:11:28 PDT)
- Albert (Fri Aug 12 2016 - 06:33:22 PDT)
[AMBER] LEaP and PARMSETs
- Aronica, Pietro (Thu Aug 18 2016 - 01:49:50 PDT)
[AMBER] LINMIN FAILURE on large protein minimization with GB and explicit
- David A Case (Fri Aug 12 2016 - 05:27:23 PDT)
- Ross Walker (Thu Aug 11 2016 - 18:47:20 PDT)
- SUNHEE CHO (Thu Aug 11 2016 - 18:25:19 PDT)
[AMBER] lipid simulation with Lipid14 FF failed
- Ross Walker (Tue Aug 16 2016 - 07:07:30 PDT)
- Albert (Tue Aug 16 2016 - 06:07:56 PDT)
- David A Case (Tue Aug 16 2016 - 05:11:16 PDT)
- Albert (Tue Aug 16 2016 - 03:00:50 PDT)
[AMBER] lowering the temperature
- Carlos Simmerling (Wed Aug 31 2016 - 04:02:04 PDT)
- Thomas Evangelidis (Wed Aug 31 2016 - 03:33:26 PDT)
- Carlos Simmerling (Tue Aug 30 2016 - 17:19:14 PDT)
- Thomas Evangelidis (Tue Aug 30 2016 - 16:51:40 PDT)
[AMBER] MASK with distance in AMBER.
- Daniel Roe (Wed Aug 17 2016 - 09:38:20 PDT)
- Parviz Seifpanahi Shabane (Tue Aug 16 2016 - 11:23:32 PDT)
- Daniel Roe (Fri Aug 12 2016 - 10:54:05 PDT)
- Parviz Seifpanahi Shabane (Fri Aug 12 2016 - 08:48:32 PDT)
[AMBER] MD simulation with non natural amino acid, parameterized using the RED server
- FyD (Sat Aug 20 2016 - 01:55:11 PDT)
- Cecilia Lindgren (Thu Aug 18 2016 - 03:40:21 PDT)
- Bill Ross (Thu Aug 18 2016 - 02:24:14 PDT)
- Hannes Loeffler (Thu Aug 18 2016 - 02:19:35 PDT)
- Bill Ross (Thu Aug 18 2016 - 02:17:30 PDT)
- Cecilia Lindgren (Thu Aug 18 2016 - 02:03:43 PDT)
- Bill Ross (Thu Aug 18 2016 - 01:49:43 PDT)
- Cecilia Lindgren (Thu Aug 18 2016 - 01:35:54 PDT)
- Bill Ross (Wed Aug 17 2016 - 23:40:44 PDT)
- Cecilia Lindgren (Wed Aug 17 2016 - 23:11:15 PDT)
- David A Case (Wed Aug 17 2016 - 07:13:46 PDT)
- Cecilia Lindgren (Wed Aug 17 2016 - 05:56:24 PDT)
[AMBER] minimum restraint_wt.
- David A Case (Tue Aug 23 2016 - 04:49:54 PDT)
- Saman Yousuf ali (Sun Aug 21 2016 - 00:05:43 PDT)
[AMBER] MMPBSA.py CalcError on ligand contribution only
- Jason Swails (Thu Aug 25 2016 - 17:19:27 PDT)
- Leandro Bortot (Thu Aug 25 2016 - 12:51:54 PDT)
- Jason Swails (Thu Aug 25 2016 - 10:35:26 PDT)
- Leandro Bortot (Thu Aug 25 2016 - 07:43:11 PDT)
[AMBER] MMPBSA.py TrajError: Could not find number of frames in .mdcrd
- maryam azimzadehirani (Mon Aug 08 2016 - 00:27:58 PDT)
- David A Case (Fri Aug 05 2016 - 04:49:56 PDT)
- maryam azimzadehirani (Thu Aug 04 2016 - 20:52:07 PDT)
[AMBER] modeling flexible loops in protein-DNA complexes
- Vlad Cojocaru (Fri Aug 12 2016 - 01:43:23 PDT)
[AMBER] Multihist in watershell command
- Damiano Spadoni (Wed Aug 31 2016 - 08:45:21 PDT)
- Daniel Roe (Fri Aug 26 2016 - 11:11:06 PDT)
- Hai Nguyen (Fri Aug 26 2016 - 10:35:39 PDT)
- Damiano Spadoni (Fri Aug 26 2016 - 05:26:24 PDT)
[AMBER] not sure if this is an ERROR in installation please suggest
- Hai Nguyen (Fri Aug 12 2016 - 06:36:34 PDT)
- Vaibhav Dixit (Fri Aug 12 2016 - 00:43:29 PDT)
- Hai Nguyen (Thu Aug 11 2016 - 22:11:31 PDT)
- Ross Walker (Thu Aug 11 2016 - 21:32:26 PDT)
- Vaibhav Dixit (Thu Aug 11 2016 - 20:44:07 PDT)
[AMBER] Off , mol2 and frcmod files
- David A Case (Tue Aug 09 2016 - 06:56:40 PDT)
- Christopher Jesudason (Tue Aug 09 2016 - 04:40:25 PDT)
[AMBER] Optimal force constant for AMBER
- David A Case (Fri Aug 12 2016 - 07:40:46 PDT)
- Stregone (Fri Aug 12 2016 - 06:29:15 PDT)
[AMBER] Output Files
- Hai Nguyen (Mon Aug 22 2016 - 20:33:37 PDT)
- Wong Li Zhe (Mon Aug 22 2016 - 18:03:36 PDT)
[AMBER] output of MMPBSA.py
- Bilal Nizami (Thu Aug 25 2016 - 03:54:19 PDT)
- Markus Kaukonen (Thu Aug 25 2016 - 03:43:20 PDT)
[AMBER] paper describing the ff15ipq protein force field is now available
- David Cerutti (Wed Aug 10 2016 - 11:55:11 PDT)
- David A Case (Wed Aug 10 2016 - 11:11:08 PDT)
[AMBER] Parameters for modified nucleosides
- Tomek Wlodarski (Tue Aug 30 2016 - 10:34:09 PDT)
[AMBER] parmchk vs parmchk2
- Hannes Loeffler (Mon Aug 15 2016 - 00:39:45 PDT)
- Andrew.Warden.csiro.au (Thu Aug 04 2016 - 18:08:21 PDT)
- David A Case (Wed Aug 03 2016 - 16:34:34 PDT)
- Andrew.Warden.csiro.au (Tue Aug 02 2016 - 21:53:09 PDT)
[AMBER] parmchk2 issue
- David A Case (Tue Aug 16 2016 - 14:15:52 PDT)
- Hannes Loeffler (Tue Aug 16 2016 - 06:47:21 PDT)
- David A Case (Tue Aug 16 2016 - 05:09:37 PDT)
- Hannes Loeffler (Tue Aug 16 2016 - 01:35:08 PDT)
- David A Case (Mon Aug 15 2016 - 09:06:35 PDT)
- Hannes Loeffler (Mon Aug 15 2016 - 08:06:38 PDT)
[AMBER] percentages of protein secondary structure.
- Hai Nguyen (Fri Aug 19 2016 - 07:51:53 PDT)
- Nhai (Thu Aug 18 2016 - 22:32:00 PDT)
- Saman Yousuf ali (Thu Aug 18 2016 - 21:17:59 PDT)
[AMBER] phi-psi distribution
- Thakur, Abhishek (Mon Aug 08 2016 - 13:54:24 PDT)
[AMBER] Problem in charge generation through antechamber
- FyD (Sat Aug 20 2016 - 02:08:20 PDT)
- Bruno Falcone (Fri Aug 19 2016 - 07:47:05 PDT)
- ATUL KUMAR (Thu Aug 18 2016 - 23:11:14 PDT)
- Bruno Falcone (Thu Aug 18 2016 - 12:58:42 PDT)
- David A Case (Thu Aug 18 2016 - 12:43:09 PDT)
- ATUL KUMAR (Thu Aug 18 2016 - 12:43:07 PDT)
- Bruno Falcone (Thu Aug 18 2016 - 12:33:49 PDT)
- ATUL KUMAR (Thu Aug 18 2016 - 11:53:45 PDT)
[AMBER] problem upon optimization
- giulia palermo (Thu Aug 25 2016 - 15:34:15 PDT)
- Jason Swails (Thu Aug 25 2016 - 10:34:44 PDT)
- Adrian Roitberg (Thu Aug 25 2016 - 08:14:34 PDT)
- giulia palermo (Thu Aug 25 2016 - 08:12:39 PDT)
[AMBER] Problem when visualizing bonds in VMD
- Nhai (Fri Aug 19 2016 - 14:53:17 PDT)
- Xiaoliu Zhang (Fri Aug 19 2016 - 13:30:22 PDT)
- Hai Nguyen (Thu Aug 18 2016 - 15:12:22 PDT)
- Xiaoliu Zhang (Thu Aug 18 2016 - 14:56:00 PDT)
- Jason Swails (Wed Aug 17 2016 - 13:17:27 PDT)
- Xiaoliu Zhang (Wed Aug 17 2016 - 12:40:22 PDT)
[AMBER] Problem with atommap function in cpptraj (v16)
- Daniel Roe (Wed Aug 31 2016 - 06:12:00 PDT)
- Samuel Bowerman (Tue Aug 30 2016 - 12:39:05 PDT)
- Daniel Roe (Fri Aug 26 2016 - 13:40:24 PDT)
- Samuel Bowerman (Tue Aug 23 2016 - 12:23:56 PDT)
[AMBER] Problem with rst7
- Carlos Simmerling (Thu Aug 25 2016 - 04:31:25 PDT)
- Elisa Pieri (Thu Aug 25 2016 - 04:04:18 PDT)
- Carlos Simmerling (Thu Aug 25 2016 - 03:33:54 PDT)
- Bill Ross (Thu Aug 25 2016 - 02:41:46 PDT)
- Elisa Pieri (Thu Aug 25 2016 - 02:12:46 PDT)
[AMBER] QM region has an odd number of electrons
- Dr. Andreas W. Goetz (Wed Aug 17 2016 - 16:33:24 PDT)
- Corum, Katharine W (Wed Aug 17 2016 - 14:22:53 PDT)
[AMBER] QM/MM energy units?
- Corum, Katharine W (Wed Aug 31 2016 - 08:58:56 PDT)
- Adrian Roitberg (Wed Aug 31 2016 - 08:56:48 PDT)
- Jacopo Sgrignani (Wed Aug 31 2016 - 08:56:24 PDT)
- Corum, Katharine W (Wed Aug 31 2016 - 08:52:45 PDT)
[AMBER] QM/MM stops at step 2114
- Corum, Katharine W (Tue Aug 16 2016 - 06:40:23 PDT)
- David A Case (Mon Aug 15 2016 - 09:13:44 PDT)
- Corum, Katharine W (Mon Aug 15 2016 - 08:08:25 PDT)
[AMBER] QMMM MD, Simulation does not start
- Stregone (Mon Aug 08 2016 - 01:20:03 PDT)
- Daniel Roe (Sun Aug 07 2016 - 14:42:01 PDT)
- Stregone (Sun Aug 07 2016 - 04:01:57 PDT)
- Dr. Andreas W. Goetz (Fri Aug 05 2016 - 14:31:45 PDT)
- Stregone (Fri Aug 05 2016 - 06:29:59 PDT)
[AMBER] query regarding restraint on specific residues.
- Saman Yousuf ali (Tue Aug 09 2016 - 08:08:10 PDT)
- David A Case (Tue Aug 09 2016 - 05:02:10 PDT)
- Saman Yousuf ali (Tue Aug 09 2016 - 00:00:57 PDT)
[AMBER] Question about usage of external QM in QM/MM
- Dr. Andreas W. Goetz (Tue Aug 09 2016 - 15:39:00 PDT)
- Fabrício Bracht (Tue Aug 09 2016 - 13:26:01 PDT)
- David A Case (Tue Aug 09 2016 - 12:27:00 PDT)
- Fabrício Bracht (Tue Aug 09 2016 - 07:13:42 PDT)
- Fabrício Bracht (Tue Aug 09 2016 - 07:07:55 PDT)
- Dr. Andreas W. Goetz (Sat Aug 06 2016 - 13:18:13 PDT)
- Fabrício Bracht (Fri Aug 05 2016 - 18:30:56 PDT)
- Dr. Andreas W. Goetz (Fri Aug 05 2016 - 14:17:21 PDT)
- Fabrício Bracht (Fri Aug 05 2016 - 11:06:18 PDT)
- David A Case (Fri Aug 05 2016 - 06:50:55 PDT)
- Dr. Andreas W. Goetz (Thu Aug 04 2016 - 23:15:40 PDT)
- Fabrício Bracht (Thu Aug 04 2016 - 19:04:46 PDT)
- David A Case (Thu Aug 04 2016 - 14:38:07 PDT)
- Fabrício Bracht (Thu Aug 04 2016 - 13:03:56 PDT)
- Fabrício Bracht (Thu Aug 04 2016 - 12:29:35 PDT)
- Dr. Andreas W. Goetz (Thu Aug 04 2016 - 12:17:15 PDT)
- Fabrício Bracht (Thu Aug 04 2016 - 10:59:10 PDT)
[AMBER] Question of Parameter Defaults
- Robert Molt (Mon Aug 15 2016 - 10:49:12 PDT)
- David A Case (Sat Aug 13 2016 - 12:48:59 PDT)
- Carlos Simmerling (Sat Aug 13 2016 - 07:37:00 PDT)
- Robert Molt (Fri Aug 12 2016 - 18:00:57 PDT)
[AMBER] Regarding antechamber command Error
- David A Case (Fri Aug 12 2016 - 05:34:01 PDT)
- Vishal Nemaysh (Thu Aug 11 2016 - 23:36:29 PDT)
- David A Case (Thu Aug 11 2016 - 12:38:51 PDT)
- Vishal Nemaysh (Thu Aug 11 2016 - 06:07:53 PDT)
- David A Case (Thu Aug 11 2016 - 04:52:43 PDT)
- Vishal Nemaysh (Wed Aug 10 2016 - 08:47:05 PDT)
[AMBER] Regarding hbond bridgeout
- Daniel Roe (Fri Aug 26 2016 - 13:24:08 PDT)
- Indrajit Deb (Wed Aug 24 2016 - 09:04:17 PDT)
[AMBER] Regarding the free energy calculation
- Daniel Mermelstein (Fri Aug 19 2016 - 11:32:23 PDT)
- Sivanandam M (Tue Aug 16 2016 - 11:00:06 PDT)
[AMBER] Regarding the use of sed command to replace water
- Budhathoki, Dipesh (Wed Aug 31 2016 - 14:54:40 PDT)
- David A Case (Wed Aug 31 2016 - 13:38:16 PDT)
- Adrian Roitberg (Wed Aug 31 2016 - 12:58:29 PDT)
- Corum, Katharine W (Wed Aug 31 2016 - 12:57:43 PDT)
- Budhathoki, Dipesh (Wed Aug 31 2016 - 12:52:37 PDT)
[AMBER] repair mdcrd?
- Daniel Roe (Thu Aug 25 2016 - 16:56:44 PDT)
- Bill Ross (Thu Aug 25 2016 - 15:48:11 PDT)
- Hai Nguyen (Thu Aug 25 2016 - 13:47:07 PDT)
- Bill Ross (Thu Aug 25 2016 - 13:26:01 PDT)
[AMBER] Restarting a crushed run
- Ross Walker (Tue Aug 16 2016 - 15:53:43 PDT)
- Bill Ross (Tue Aug 16 2016 - 14:24:52 PDT)
- Dmitry Suplatov (Tue Aug 16 2016 - 13:27:34 PDT)
- Dmitry Suplatov (Tue Aug 16 2016 - 12:45:23 PDT)
- Bill Ross (Tue Aug 16 2016 - 12:40:07 PDT)
- Bill Ross (Tue Aug 16 2016 - 12:12:05 PDT)
- DmitryASuplatov (Tue Aug 16 2016 - 09:43:44 PDT)
[AMBER] restraining mean square displacements
- Adrian Roitberg (Fri Aug 05 2016 - 12:54:33 PDT)
- Irem Altan (Fri Aug 05 2016 - 12:52:35 PDT)
[AMBER] restraint does not work in mininmization
- Hirdesh Kumar (Tue Aug 30 2016 - 01:02:56 PDT)
- Michael Shokhen (Tue Aug 30 2016 - 00:48:54 PDT)
[AMBER] reweighting scheme
- Thakur, Abhishek (Mon Aug 08 2016 - 12:02:00 PDT)
[AMBER] RMSd
- Bill Ross (Wed Aug 17 2016 - 23:18:53 PDT)
- Wong Li Zhe (Wed Aug 17 2016 - 22:50:22 PDT)
- Wong Li Zhe (Wed Aug 17 2016 - 21:12:52 PDT)
- Hai Nguyen (Wed Aug 17 2016 - 21:11:05 PDT)
- Wong Li Zhe (Wed Aug 17 2016 - 21:08:05 PDT)
[AMBER] running RISM/MD on multi processors
- Tyler Luchko (Lists) (Tue Aug 02 2016 - 14:46:02 PDT)
- Jingyi Yan (Tue Aug 02 2016 - 14:26:16 PDT)
[AMBER] Running tleap with old prmtop
- Samuel Bowerman (Thu Aug 11 2016 - 10:30:18 PDT)
- Taylor Quinn (Thu Aug 11 2016 - 10:13:09 PDT)
[AMBER] Sander bomb: how to create a larger box
- Ruth Helena Tichauer (Tue Aug 02 2016 - 07:14:33 PDT)
- David A Case (Mon Aug 01 2016 - 07:57:05 PDT)
- Ruth Helena Tichauer (Mon Aug 01 2016 - 05:38:12 PDT)
- Bill Ross (Mon Aug 01 2016 - 05:11:10 PDT)
- Ruth Helena Tichauer (Mon Aug 01 2016 - 04:42:28 PDT)
- Bill Ross (Mon Aug 01 2016 - 04:32:22 PDT)
- Ruth Helena Tichauer (Mon Aug 01 2016 - 03:53:51 PDT)
[AMBER] save Hessian nmode mmpbsa
- Jason Swails (Thu Aug 04 2016 - 10:56:37 PDT)
- Bruno Falcone (Thu Aug 04 2016 - 08:45:51 PDT)
- Bruno Falcone (Wed Aug 03 2016 - 09:51:23 PDT)
[AMBER] secondary structure graph vs Time
- Parviz Seifpanahi Shabane (Tue Aug 16 2016 - 08:45:59 PDT)
- Daniel Roe (Mon Aug 15 2016 - 14:15:24 PDT)
- Parviz Seifpanahi Shabane (Mon Aug 15 2016 - 13:28:43 PDT)
- Prajwal Nandekar (Fri Aug 12 2016 - 01:58:20 PDT)
- Adrian Roitberg (Thu Aug 11 2016 - 09:26:20 PDT)
- Parviz Seifpanahi Shabane (Thu Aug 11 2016 - 09:16:59 PDT)
- Adrian Roitberg (Thu Aug 11 2016 - 09:05:01 PDT)
- Parviz Seifpanahi Shabane (Thu Aug 11 2016 - 09:03:01 PDT)
[AMBER] SEP parameter with ff15ipq
- Carlos Simmerling (Fri Aug 26 2016 - 06:35:52 PDT)
- vadiraj kurdekar (Thu Aug 25 2016 - 21:43:22 PDT)
- David Cerutti (Thu Aug 25 2016 - 07:18:37 PDT)
- David A Case (Thu Aug 25 2016 - 06:33:47 PDT)
- vadiraj kurdekar (Thu Aug 25 2016 - 00:08:31 PDT)
[AMBER] Setting up a pdb file for a QM/MM calculation with explicit water
- David A Case (Tue Aug 09 2016 - 12:30:04 PDT)
- Corum, Katharine W (Tue Aug 09 2016 - 07:53:51 PDT)
- Marc van der Kamp (Tue Aug 09 2016 - 07:43:13 PDT)
- Corum, Katharine W (Tue Aug 09 2016 - 07:20:05 PDT)
- David A Case (Tue Aug 09 2016 - 04:52:06 PDT)
- Ayesha Fatima (Mon Aug 08 2016 - 16:36:48 PDT)
- Corum, Katharine W (Mon Aug 08 2016 - 14:33:12 PDT)
[AMBER] Sigma and epsilon vdw parameters
- Bill Ross (Mon Aug 22 2016 - 15:58:45 PDT)
- Neha Gandhi (Mon Aug 22 2016 - 15:28:44 PDT)
[AMBER] Simulation Time
- Dd H (Wed Aug 24 2016 - 04:31:07 PDT)
- Wong Li Zhe (Mon Aug 22 2016 - 22:00:03 PDT)
[AMBER] simultaneous use of ibelly=1 and ntr=1
- Saman Yousuf ali (Tue Aug 09 2016 - 12:41:00 PDT)
- David A Case (Tue Aug 09 2016 - 12:33:05 PDT)
- Saman Yousuf ali (Tue Aug 09 2016 - 08:54:47 PDT)
[AMBER] SMD simulation
- bharat gupta (Sun Aug 07 2016 - 22:44:08 PDT)
[AMBER] solid surface simulation in amber
- Neha Gandhi (Mon Aug 22 2016 - 03:17:23 PDT)
- Bill Ross (Mon Aug 22 2016 - 03:07:59 PDT)
- Neha Gandhi (Mon Aug 22 2016 - 02:00:52 PDT)
- Bill Ross (Fri Aug 19 2016 - 18:35:12 PDT)
- Neha Gandhi (Fri Aug 19 2016 - 18:28:18 PDT)
- Bill Ross (Fri Aug 19 2016 - 14:06:40 PDT)
- David A Case (Fri Aug 19 2016 - 07:54:01 PDT)
- Neha Gandhi (Fri Aug 19 2016 - 01:57:24 PDT)
- David A Case (Thu Aug 18 2016 - 06:13:05 PDT)
- Bill Ross (Thu Aug 18 2016 - 01:55:20 PDT)
- Neha Gandhi (Thu Aug 18 2016 - 01:48:12 PDT)
- Bill Ross (Thu Aug 18 2016 - 01:36:32 PDT)
- Neha Gandhi (Thu Aug 18 2016 - 01:27:28 PDT)
- Daniel Roe (Tue Aug 16 2016 - 07:58:05 PDT)
- Neha Gandhi (Tue Aug 16 2016 - 06:17:47 PDT)
- David A Case (Tue Aug 16 2016 - 05:04:29 PDT)
- Bill Ross (Tue Aug 16 2016 - 01:27:51 PDT)
- Neha Gandhi (Tue Aug 16 2016 - 01:00:20 PDT)
- Bill Ross (Tue Aug 16 2016 - 00:33:02 PDT)
- Neha Gandhi (Mon Aug 15 2016 - 22:25:46 PDT)
- David A Case (Mon Aug 15 2016 - 04:39:23 PDT)
- Neha Gandhi (Sun Aug 14 2016 - 23:59:57 PDT)
[AMBER] solvate hexagonal box
- Neha Gandhi (Wed Aug 03 2016 - 22:29:52 PDT)
[AMBER] subject: parametrization of Force field
- David A Case (Tue Aug 02 2016 - 07:36:09 PDT)
- DOCENTE ANTISTIO ANIBAL ALVIS AMADOR (Mon Aug 01 2016 - 07:50:08 PDT)
[AMBER] Temperature Shoot-up in TMD
- Carlos Simmerling (Fri Aug 19 2016 - 04:50:38 PDT)
- Bill Ross (Fri Aug 19 2016 - 00:20:52 PDT)
- Aravind Ravichandran (Fri Aug 19 2016 - 00:26:24 PDT)
[AMBER] the end phosphoric acid group is deformed during simulation
- rain (Tue Aug 02 2016 - 17:12:34 PDT)
[AMBER] the phosphoric acid group is deformed
- 乔艳 (Tue Aug 02 2016 - 16:40:30 PDT)
[AMBER] tinker_to_amber error
- Xiaoliu Zhang (Wed Aug 03 2016 - 07:46:04 PDT)
- Ray Luo (Mon Aug 01 2016 - 10:40:08 PDT)
- Xiaoliu Zhang (Mon Aug 01 2016 - 08:52:17 PDT)
[AMBER] Tutorial B5 - Loading CRO from ccif file
- Alfredo Quevedo (Fri Aug 19 2016 - 10:49:05 PDT)
- David A Case (Fri Aug 19 2016 - 10:43:15 PDT)
- Alfredo Quevedo (Fri Aug 19 2016 - 07:26:42 PDT)
[AMBER] Two ion problem with mcpb.py
- Abhilash J (Thu Aug 18 2016 - 21:19:44 PDT)
- Pengfei Li (Thu Aug 18 2016 - 18:18:35 PDT)
- Abhilash J (Thu Aug 18 2016 - 12:17:50 PDT)
- Pengfei Li (Tue Aug 16 2016 - 07:40:46 PDT)
- sunita guptacDgug (Fri Aug 12 2016 - 12:50:46 PDT)
- Abhilash J (Fri Aug 12 2016 - 10:11:55 PDT)
[AMBER] umbrella sampling restraining both angle and distance
- Carlos Simmerling (Sun Aug 14 2016 - 07:55:57 PDT)
- Thakur, Abhishek (Fri Aug 12 2016 - 15:49:30 PDT)
- Carlos Simmerling (Fri Aug 12 2016 - 15:22:27 PDT)
- Thakur, Abhishek (Fri Aug 12 2016 - 09:50:11 PDT)
[AMBER] unreadable crd files
- Hai Nguyen (Thu Aug 04 2016 - 21:05:07 PDT)
- Adrian Roitberg (Thu Aug 04 2016 - 15:31:29 PDT)
- macc_200 (Thu Aug 04 2016 - 14:47:48 PDT)
[AMBER] Use two different force fields in Amber
- Xiaoliu Zhang (Fri Aug 05 2016 - 08:30:56 PDT)
- David A Case (Tue Aug 02 2016 - 07:34:33 PDT)
- Xiaoliu Zhang (Mon Aug 01 2016 - 07:41:19 PDT)
[AMBER] Water flexibility in QM/MM simulation
- Ruth Helena Tichauer (Tue Aug 16 2016 - 09:27:14 PDT)
[AMBER] WHAM analysis
- Adrian Roitberg (Sat Aug 20 2016 - 11:17:23 PDT)
- Chi Jin (Sat Aug 20 2016 - 11:13:41 PDT)
- Amy Rice (Sat Aug 20 2016 - 08:41:00 PDT)
- Chi Jin (Sat Aug 20 2016 - 00:30:05 PDT)
- Thakur, Abhishek (Fri Aug 19 2016 - 14:55:16 PDT)
[AMBER] What cutoff you use in Amber simulations?
- Jason Swails (Fri Aug 19 2016 - 05:57:48 PDT)
- DmitryASuplatov (Fri Aug 19 2016 - 04:35:40 PDT)
[AMBER] which forcefield it is?
- Ross Walker (Tue Aug 02 2016 - 09:22:05 PDT)
- Amy Rice (Tue Aug 02 2016 - 09:17:43 PDT)
- Albert (Mon Aug 01 2016 - 23:38:43 PDT)
[AMBER] {AMBER} installation on mac osx 10.11.6 hanging when configuring NetCDF
- mirko hennig (Tue Aug 09 2016 - 08:29:50 PDT)
- David A Case (Tue Aug 09 2016 - 05:00:39 PDT)
- mirko hennig (Tue Aug 09 2016 - 00:53:23 PDT)
Problems to calculate frequencies
- David A Case (Thu Aug 25 2016 - 06:40:56 PDT)
- Stregone (Thu Aug 25 2016 - 03:14:42 PDT)

Amber Archive Aug 2016 by subject