Amber Archive May 2019: by subject

[AMBER] 3D-RISM options
- Tyler Luchko (Lists) (Wed May 15 2019 - 10:17:12 PDT)
- Ryan Pavlovicz (Wed May 15 2019 - 07:45:41 PDT)
- David A Case (Wed May 15 2019 - 05:46:55 PDT)
- Ryan Pavlovicz (Tue May 14 2019 - 23:01:18 PDT)
- Tyler Luchko (Lists) (Tue May 14 2019 - 17:17:38 PDT)
- Ryan Pavlovicz (Tue May 14 2019 - 17:10:31 PDT)
- Tyler Luchko (Lists) (Tue May 14 2019 - 15:44:24 PDT)
- Ryan Pavlovicz (Tue May 14 2019 - 14:45:27 PDT)
[AMBER] [mjldehoon.yahoo.com: Files for Tutorial 32 (Deriving bonded parameters with mdgx)]
- David Cerutti (Fri May 03 2019 - 08:30:40 PDT)
[AMBER] amber 16 installation on Ubuntu 18
- David A Case (Wed May 29 2019 - 04:58:12 PDT)
- Ming Tang (Tue May 28 2019 - 21:45:12 PDT)
[AMBER] AMBER 16 vs 18 on different cuda
- David Cerutti (Wed May 08 2019 - 13:17:12 PDT)
- Xiaoyu Wang (Wed May 08 2019 - 13:08:11 PDT)
[AMBER] AMBER Digest, Vol 2638, Issue 1
- ali akbar (Tue May 07 2019 - 22:07:54 PDT)
[AMBER] amber inputs
- David A Case (Thu May 23 2019 - 07:59:33 PDT)
- Sina (Thu May 23 2019 - 06:44:31 PDT)
[AMBER] amber18 parallel cpu make test hanging at first test
- Ravi Abrol (Tue May 14 2019 - 17:55:22 PDT)
- David A Case (Tue May 14 2019 - 06:02:37 PDT)
- Ravi Abrol (Mon May 13 2019 - 11:47:18 PDT)
[AMBER] AmberTools hardcodes library names into binaries
- David Case (Sat May 04 2019 - 19:19:14 PDT)
- viktor drobot (Sat May 04 2019 - 03:57:57 PDT)
[AMBER] Ambertools2018/SQM installation
- Sina (Mon May 06 2019 - 09:24:44 PDT)
- David A Case (Mon May 06 2019 - 07:43:50 PDT)
- Gustaf Olsson (Mon May 06 2019 - 03:36:28 PDT)
- Sina (Mon May 06 2019 - 01:59:31 PDT)
[AMBER] Any help on how to implement it in cpptraj?
- Daniel Roe (Thu May 09 2019 - 11:54:48 PDT)
- Debarati DasGupta (Mon May 06 2019 - 13:27:46 PDT)
[AMBER] anybody has any idea?
- Albert (Thu May 30 2019 - 04:14:51 PDT)
- David A Case (Thu May 30 2019 - 04:04:26 PDT)
- Albert (Thu May 30 2019 - 00:17:35 PDT)
[AMBER] Are R.E.D. tools still a thing?
- Jason Swails (Fri May 10 2019 - 12:23:47 PDT)
- Feng, Zimin (Fri May 03 2019 - 10:52:09 PDT)
- Luca Codutti (Fri May 03 2019 - 10:17:35 PDT)
[AMBER] Atom type (C.2) is not in PARMCHK.DAT Segmentation fault (core dumped)
- Sadaf Rani (Wed May 15 2019 - 11:00:28 PDT)
- David A Case (Tue May 14 2019 - 05:55:43 PDT)
- Sadaf Rani (Mon May 13 2019 - 08:56:06 PDT)
[AMBER] Average structure vs Individual frames
- David A Case (Tue May 14 2019 - 06:09:05 PDT)
- Bill Ross (Mon May 13 2019 - 19:53:18 PDT)
- Yin, Guowei (Mon May 13 2019 - 19:19:16 PDT)
- Bill Ross (Mon May 13 2019 - 18:50:15 PDT)
- Yin, Guowei (Mon May 13 2019 - 18:16:59 PDT)
[AMBER] Boron QM/MM
- Pär Håkansson (Fri May 31 2019 - 05:55:05 PDT)
- Pär Håkansson (Fri May 31 2019 - 04:08:00 PDT)
[AMBER] Bubbles during NPT and NVT simulations
- David A Case (Thu May 16 2019 - 05:05:25 PDT)
- Bill Ross (Thu May 16 2019 - 03:13:54 PDT)
- Carlos Simmerling (Thu May 16 2019 - 03:02:03 PDT)
- Stefano Motta (Thu May 16 2019 - 02:56:24 PDT)
[AMBER] Building inpcrd and prmtop for a non-standard residue containing cyclic peptide
- Schröder, David Christopher (Tue May 14 2019 - 07:20:27 PDT)
- David A Case (Tue May 14 2019 - 06:12:31 PDT)
- Pietro Aronica (Tue May 14 2019 - 02:19:31 PDT)
[AMBER] Capping a dipeptide with Boc
- Saikat Pal (Wed May 08 2019 - 09:44:32 PDT)
- Alessandro Contini (Wed May 08 2019 - 09:29:09 PDT)
- Saikat Pal (Wed May 08 2019 - 09:16:24 PDT)
- Alessandro Contini (Wed May 08 2019 - 07:33:38 PDT)
- Saikat Pal (Wed May 08 2019 - 05:15:12 PDT)
- Alessandro Contini (Wed May 08 2019 - 04:14:46 PDT)
- Saikat Pal (Wed May 08 2019 - 04:04:50 PDT)
[AMBER] Catalysis mechanism of ATPase
- Pratul Agarwal (Mon May 20 2019 - 15:59:27 PDT)
- sunyeping (Sun May 19 2019 - 04:29:35 PDT)
[AMBER] Center of mass velocity autocorrelation function
- Reber, David (Sun May 12 2019 - 18:29:33 PDT)
[AMBER] Changes to AmberTools antechamber Makefile
- David A Case (Wed May 29 2019 - 04:57:05 PDT)
- Jocelyn Sunseri (Tue May 28 2019 - 10:58:47 PDT)
[AMBER] check version
- David Case (Sun May 05 2019 - 13:38:36 PDT)
- Pratul Agarwal (Sun May 05 2019 - 07:51:40 PDT)
- Akshay Prabhakant (Sun May 05 2019 - 05:29:29 PDT)
[AMBER] compiling Amber Tools 19
- Hashemi, Mohtadin (Thu May 30 2019 - 12:12:16 PDT)
- Hai Nguyen (Thu May 30 2019 - 11:22:52 PDT)
- Hashemi, Mohtadin (Thu May 30 2019 - 06:59:59 PDT)
- Vlad Cojocaru (Tue May 28 2019 - 05:37:07 PDT)
- David A Case (Tue May 28 2019 - 04:38:55 PDT)
- Vlad Cojocaru (Tue May 28 2019 - 01:33:15 PDT)
- David Case (Mon May 27 2019 - 18:45:21 PDT)
- Vlad Cojocaru (Mon May 27 2019 - 05:14:32 PDT)
- Vlad Cojocaru (Mon May 27 2019 - 04:42:38 PDT)
[AMBER] continuous DNA
- Thomas C. Bishop (Thu May 09 2019 - 12:33:40 PDT)
- David A Case (Thu May 09 2019 - 10:44:04 PDT)
- Qinghua Liao (Thu May 09 2019 - 06:39:00 PDT)
[AMBER] CPPTRAJ average residue-wise contact map
- anu chandra (Thu May 02 2019 - 08:30:48 PDT)
- Daniel Roe (Thu May 02 2019 - 05:25:25 PDT)
- anu chandra (Wed May 01 2019 - 12:06:24 PDT)
[AMBER] CPPTRAJ gnu extension not working
- Daniel Roe (Thu May 02 2019 - 05:34:12 PDT)
[AMBER] CPPTRAJ OPENMP - MPI
- Daniel Roe (Wed May 08 2019 - 04:23:21 PDT)
- Lorenzo Gontrani (Wed May 08 2019 - 02:51:34 PDT)
[AMBER] Crashed dynamics : connectivity
- David A Case (Wed May 15 2019 - 07:50:27 PDT)
- emanuele falbo (Wed May 15 2019 - 05:59:49 PDT)
[AMBER] cuda test failing after installation
- Ravi Abrol (Mon May 13 2019 - 11:52:43 PDT)
- Ravi Abrol (Tue May 07 2019 - 12:43:28 PDT)
- David Cerutti (Tue May 07 2019 - 11:02:48 PDT)
- Ravi Abrol (Tue May 07 2019 - 10:26:54 PDT)
[AMBER] deselect residues for step1 model in MCPB.py
- SARAH JEANNE LEFAVE (Wed May 29 2019 - 09:39:30 PDT)
[AMBER] different energy values from mdout and cpptraj
- David A Case (Tue May 07 2019 - 06:01:20 PDT)
- Batuhan Kav (Tue May 07 2019 - 05:24:18 PDT)
[AMBER] Different potential energies between recomputed and original simulations from PMEMD?
- 杨明俊 (Fri May 24 2019 - 05:02:28 PDT)
- 杨明俊 (Fri May 24 2019 - 03:14:32 PDT)
[AMBER] Distance calculation and distance matrix giving discrepant results
- Jonathan Huihui (Fri May 03 2019 - 10:01:27 PDT)
- Daniel Roe (Fri May 03 2019 - 09:14:29 PDT)
- Jonathan Huihui (Thu May 02 2019 - 09:25:55 PDT)
[AMBER] distance restraint failed in minimization and MD
- David A Case (Wed May 08 2019 - 05:09:24 PDT)
- wujue (Tue May 07 2019 - 19:38:40 PDT)
[AMBER] DRMSD utility in cpptraj
- Debarati DasGupta (Tue May 21 2019 - 06:15:48 PDT)
- Daniel Roe (Mon May 20 2019 - 12:33:46 PDT)
- Debarati DasGupta (Fri May 17 2019 - 13:45:30 PDT)
[AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file
- Joan Torras (Fri May 17 2019 - 03:47:00 PDT)
- Gargi Borgohain (Fri May 17 2019 - 02:45:31 PDT)
- Charles Lin (Thu May 16 2019 - 08:06:50 PDT)
- Bill Ross (Thu May 16 2019 - 03:03:55 PDT)
- Gargi Borgohain (Thu May 16 2019 - 02:38:29 PDT)
[AMBER] empty cein file redox potential calculations
- Cruzeiro,Vinicius Wilian D (Thu May 30 2019 - 12:29:15 PDT)
- Vaibhav Dixit (Thu May 30 2019 - 07:38:16 PDT)
- Marcos Serrou do Amaral (Thu May 30 2019 - 05:38:51 PDT)
- Vaibhav Dixit (Thu May 30 2019 - 05:16:45 PDT)
- Marcos Serrou do Amaral (Thu May 30 2019 - 05:03:43 PDT)
- Vaibhav Dixit (Thu May 30 2019 - 04:36:37 PDT)
[AMBER] Energy shifted energy term
- Debarati DasGupta (Fri May 10 2019 - 13:13:59 PDT)
- Jason Swails (Fri May 10 2019 - 12:04:04 PDT)
- Debarati DasGupta (Thu May 09 2019 - 13:48:42 PDT)
[AMBER] Entropy calculation for a protein homodimerization
- Rakesh Srivastava (Wed May 15 2019 - 05:20:31 PDT)
- Pratul Agarwal (Wed May 15 2019 - 04:47:16 PDT)
- Rakesh Srivastava (Wed May 15 2019 - 01:47:53 PDT)
[AMBER] Error in step 3 of MCPB.py
- Shahila Muhammed (Wed May 22 2019 - 05:20:42 PDT)
- Pengfei Li (Tue May 21 2019 - 08:50:36 PDT)
- Shahila Muhammed (Fri May 17 2019 - 01:02:55 PDT)
[AMBER] Error using mm_pbsa.pl binding energy calculations
- Jaimes, Luis (Wed May 01 2019 - 17:44:23 PDT)
[AMBER] error with loading HEM parameters for constph redox calcuations
- Vaibhav Dixit (Fri May 31 2019 - 12:32:03 PDT)
- Vaibhav Dixit (Fri May 31 2019 - 12:05:26 PDT)
- Vaibhav Dixit (Thu May 30 2019 - 02:35:41 PDT)
- Vaibhav Dixit (Wed May 29 2019 - 13:52:32 PDT)
- David A Case (Wed May 29 2019 - 09:03:23 PDT)
- Vaibhav Dixit (Wed May 29 2019 - 07:53:28 PDT)
[AMBER] Failed to generate parameters
- Sadaf Rani (Sat May 11 2019 - 08:48:41 PDT)
[AMBER] FEW not producing *.lib file for ligand
- ali akbar (Thu May 02 2019 - 02:50:12 PDT)
[AMBER] FEW- an issue generating *.lib for ligand
- ali akbar (Sat May 04 2019 - 00:39:44 PDT)
[AMBER] Files for Tutorial 32 (Deriving bonded parameters with mdgx)
- Michiel de Hoon (Fri May 03 2019 - 02:26:58 PDT)
[AMBER] FLAG_POINTERS in prmtop file
- Jason Swails (Fri May 10 2019 - 12:25:48 PDT)
- Feng, Zimin (Fri May 03 2019 - 09:11:09 PDT)
- Feng, Zimin (Fri May 03 2019 - 08:10:33 PDT)
[AMBER] Force field for intrinsically disordered proteins
- David Case (Sun May 19 2019 - 05:24:37 PDT)
- Markowska (Sat May 18 2019 - 05:11:46 PDT)
[AMBER] Force field for nucleobases, nucleosides and nucleotides
- David A Case (Fri May 03 2019 - 06:40:36 PDT)
- Elisa Pieri (Thu May 02 2019 - 15:31:19 PDT)
- Elisa Pieri (Thu May 02 2019 - 14:10:06 PDT)
[AMBER] Fwd: August 5-8.SBU: 2019 Summer School Parallel Computing in Molecular Sciences
- Carlos Simmerling (Fri May 10 2019 - 07:09:40 PDT)
[AMBER] Fwd: The unperturbed charge of the unit: 4.003000 is not zero
- Bill Ross (Sat May 11 2019 - 12:36:57 PDT)
- Sadaf Rani (Sat May 11 2019 - 04:16:07 PDT)
[AMBER] GCC 2019, November 3-5 in Mainz, Deadline extendend to June 23, 2019
- Stefan.Guessregen.sanofi.com (Mon May 27 2019 - 23:20:14 PDT)
[AMBER] GPU versions: pmemd.cuda*
- Pratul Agarwal (Thu May 09 2019 - 08:17:08 PDT)
- Yin, Guowei (Thu May 09 2019 - 08:11:05 PDT)
[AMBER] graph
- Daniel Roe (Thu May 30 2019 - 08:08:20 PDT)
- Charu Sharma (JRF) (Mon May 27 2019 - 04:06:01 PDT)
[AMBER] Guidance on WHAM
- Daniel Fernández Remacha (Tue May 07 2019 - 11:46:45 PDT)
- Ruth Helena Tichauer (Fri May 03 2019 - 08:18:48 PDT)
- Carlos Simmerling (Fri May 03 2019 - 08:14:49 PDT)
- Ruth Helena Tichauer (Fri May 03 2019 - 08:09:38 PDT)
[AMBER] hbond lifetime filesize issues
- Reber, David (Tue May 21 2019 - 19:09:20 PDT)
- Daniel Roe (Tue May 21 2019 - 09:50:58 PDT)
- Reber, David (Wed May 15 2019 - 22:02:36 PDT)
- Reber, David (Wed May 15 2019 - 18:52:17 PDT)
- Daniel Roe (Wed May 15 2019 - 06:36:27 PDT)
- Reber, David (Wed May 15 2019 - 02:53:13 PDT)
[AMBER] Help compiling AMBER18 GPU Code- Cannot find compiler cl.exe in PATH
- David A Case (Thu May 30 2019 - 03:58:58 PDT)
- Jay Spencer (Wed May 29 2019 - 19:01:53 PDT)
[AMBER] How to generate boron atom force field parameters
- David Case (Thu May 30 2019 - 18:24:54 PDT)
- Meng Wu (Thu May 30 2019 - 03:53:24 PDT)
[AMBER] How to generate the correct force field parameter for a large molecule?
- Bill Ross (Mon May 27 2019 - 00:52:02 PDT)
- xmgign.126.com (Sun May 26 2019 - 23:27:44 PDT)
[AMBER] Installation of AMBER 18 regarding
- David A Case (Tue May 28 2019 - 10:43:50 PDT)
[AMBER] issues with pmemd.cuda
- Veenis, Andrew Jay (Fri May 03 2019 - 12:20:43 PDT)
[AMBER] jobs getting cancelled on cuda7 gpus
- maryam azimzadehirani (Fri May 24 2019 - 22:59:14 PDT)
[AMBER] Lennard Jones parameters in frcmod
- Matias Machado (Thu May 23 2019 - 08:21:56 PDT)
- Stefano Motta (Thu May 23 2019 - 07:31:17 PDT)
[AMBER] Library for Phosphate ion
- Sowmya Indrakumar (Wed May 01 2019 - 06:19:14 PDT)
- David A Case (Wed May 01 2019 - 04:44:06 PDT)
[AMBER] make test fail
- David A Case (Fri May 31 2019 - 10:21:31 PDT)
- Sadaf Rani (Fri May 31 2019 - 09:24:55 PDT)
[AMBER] matching energies betwen amber-md and gromacs using amber parameters in both
- Karl Kirschner (Tue May 07 2019 - 00:21:37 PDT)
- Akshay Prabhakant (Mon May 06 2019 - 04:11:58 PDT)
- Karl Kirschner (Mon May 06 2019 - 03:32:28 PDT)
- Akshay Prabhakant (Mon May 06 2019 - 02:59:06 PDT)
[AMBER] MC barostat cause the system to stuck indefinitely
- David A Case (Mon May 13 2019 - 05:44:29 PDT)
- Zhiyi Wu (Sat May 11 2019 - 14:10:13 PDT)
[AMBER] Minimization input
- Carlos Simmerling (Wed May 29 2019 - 03:47:35 PDT)
- Sadaf Rani (Wed May 29 2019 - 03:29:46 PDT)
[AMBER] Missing file amber tutorial
- Sadaf Rani (Tue May 28 2019 - 02:01:02 PDT)
- Pratul Agarwal (Wed May 15 2019 - 11:32:55 PDT)
- Pratul Agarwal (Wed May 15 2019 - 11:12:02 PDT)
- Sadaf Rani (Wed May 15 2019 - 11:06:10 PDT)
[AMBER] MMPBSA radiopt effect on EDISPER
- Thomas Gaillard (Mon May 13 2019 - 09:40:57 PDT)
[AMBER] mol2 files for FEW
- Nadine Homeyer (Mon May 20 2019 - 11:10:56 PDT)
- David A Case (Wed May 01 2019 - 10:50:43 PDT)
[AMBER] NetCDF trajectory file does not contain information about time/timestep
- Daniel Roe (Mon May 20 2019 - 11:08:54 PDT)
- Markowska (Sat May 18 2019 - 12:46:30 PDT)
- Daniel Roe (Fri May 17 2019 - 07:25:00 PDT)
- Markowska (Wed May 15 2019 - 11:12:57 PDT)
[AMBER] Novel Force Field Parameters for Aromatic Dihedrals
- Erdem Yeler (Fri May 03 2019 - 02:25:00 PDT)
- Carlos Simmerling (Thu May 02 2019 - 09:36:00 PDT)
[AMBER] NVidia backwards compatibility
- James Kress (Wed May 08 2019 - 06:43:11 PDT)
- David A Case (Wed May 08 2019 - 05:14:42 PDT)
- James Kress (Tue May 07 2019 - 12:43:34 PDT)
[AMBER] nvidia tesla-t4 and amber
- Luca Codutti (Wed May 15 2019 - 09:28:01 PDT)
- David Cerutti (Wed May 15 2019 - 08:58:45 PDT)
- Shenglong Wang (Wed May 15 2019 - 08:52:12 PDT)
- Luca Codutti (Wed May 15 2019 - 08:46:36 PDT)
[AMBER] Open position for doctoral candidate in biomolecular simulations
- Jan Brezovsky (Fri May 17 2019 - 02:17:10 PDT)
[AMBER] Optimization of geometry in xleap
- Bill Ross (Wed May 29 2019 - 23:36:14 PDT)
- Shilpa Gupta (Wed May 29 2019 - 23:21:05 PDT)
[AMBER] parameter file for dUTP
- David Case (Thu May 30 2019 - 18:43:37 PDT)
- Zachary Fallon (Thu May 30 2019 - 15:12:07 PDT)
- sunyeping (Thu May 30 2019 - 14:38:11 PDT)
- Zachary Fallon (Thu May 30 2019 - 10:55:20 PDT)
- sunyeping (Thu May 30 2019 - 06:03:54 PDT)
[AMBER] PCA with a really giant trajectory
- David Cerutti (Tue May 28 2019 - 11:47:56 PDT)
- Daniel Roe (Tue May 28 2019 - 11:41:52 PDT)
- David Cerutti (Tue May 28 2019 - 10:49:15 PDT)
- Chris Neale (Mon May 27 2019 - 00:29:24 PDT)
- David Cerutti (Sat May 25 2019 - 12:31:54 PDT)
[AMBER] phosphor tyrosine bound to C5' terminal DA5
- David Case (Thu May 30 2019 - 18:20:12 PDT)
- Fabian Glaser (Wed May 29 2019 - 12:15:15 PDT)
- Bill Ross (Wed May 29 2019 - 12:09:53 PDT)
- Fabian Glaser (Wed May 29 2019 - 10:54:14 PDT)
- Fabian Glaser (Wed May 29 2019 - 07:04:19 PDT)
- Bill Ross (Wed May 29 2019 - 07:12:15 PDT)
[AMBER] pmemd.cuda "cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered"
- Pratul Agarwal (Wed May 08 2019 - 09:09:44 PDT)
- Akshay Prabhakant (Wed May 08 2019 - 08:50:21 PDT)
[AMBER] Print Hessian matrix in (3,3) dimension
- David Case (Mon May 27 2019 - 18:30:38 PDT)
- Bouibes Amine (Sun May 26 2019 - 01:03:55 PDT)
[AMBER] Problem in simulating peptide with modified amino acid - vlimit exceeded
- David A Case (Tue May 28 2019 - 04:45:22 PDT)
- Saikat Dutta chowdhury (Tue May 28 2019 - 04:07:07 PDT)
[AMBER] problem of srun
- David A Case (Wed May 29 2019 - 06:45:22 PDT)
- Albert (Wed May 29 2019 - 05:51:46 PDT)
[AMBER] Problem with preparing parameters with antechamber for modified amino acid
- Saikat Dutta chowdhury (Mon May 13 2019 - 21:23:06 PDT)
- David A Case (Mon May 13 2019 - 05:51:38 PDT)
- Saikat Dutta chowdhury (Mon May 13 2019 - 03:41:15 PDT)
- Bill Ross (Mon May 13 2019 - 01:05:59 PDT)
- Bill Ross (Mon May 13 2019 - 00:56:07 PDT)
- Saikat Dutta chowdhury (Mon May 13 2019 - 00:46:40 PDT)
- Bill Ross (Sun May 12 2019 - 01:52:59 PDT)
- Saikat Dutta chowdhury (Sat May 11 2019 - 23:40:19 PDT)
[AMBER] Protein-Lipid Bilayer PDB preparation Issue(s)
- Stephan Schott (Mon May 27 2019 - 11:49:56 PDT)
- Abhishek Sirohiwal (Mon May 27 2019 - 11:31:10 PDT)
- Stephan Schott (Mon May 27 2019 - 10:17:42 PDT)
- Abhishek Sirohiwal (Mon May 27 2019 - 09:48:32 PDT)
[AMBER] Qm minimization,
- David Case (Fri May 24 2019 - 04:42:33 PDT)
- Sina (Fri May 24 2019 - 03:22:47 PDT)
[AMBER] Question about sander running parallel
- Charo del Genio (Fri May 31 2019 - 12:19:27 PDT)
- David A Case (Fri May 31 2019 - 10:31:08 PDT)
- Sadaf Rani (Fri May 31 2019 - 09:39:23 PDT)
[AMBER] Question regarding compatibility of Temperature replica exchange MD (TREMD) with constant pH MD
- Pacheco, Sayuri (Fri May 03 2019 - 13:02:06 PDT)
- Cruzeiro,Vinicius Wilian D (Fri May 03 2019 - 12:14:45 PDT)
- Pacheco, Sayuri (Fri May 03 2019 - 11:48:35 PDT)
[AMBER] Radgyr or distance averages
- Daniel Roe (Fri May 31 2019 - 07:17:28 PDT)
- Reber, David (Thu May 30 2019 - 20:55:32 PDT)
- Thomas Cheatham (Thu May 30 2019 - 20:07:06 PDT)
- Reber, David (Thu May 30 2019 - 20:03:49 PDT)
- Thomas Cheatham (Thu May 30 2019 - 19:43:02 PDT)
- Reber, David (Thu May 30 2019 - 19:33:47 PDT)
- Thomas Cheatham (Thu May 30 2019 - 19:23:11 PDT)
- Reber, David (Thu May 30 2019 - 19:17:53 PDT)
- Thomas Cheatham (Thu May 30 2019 - 19:07:01 PDT)
- Reber, David (Thu May 30 2019 - 18:46:20 PDT)
- Daniel Roe (Thu May 30 2019 - 18:39:12 PDT)
- Reber, David (Thu May 30 2019 - 18:33:31 PDT)
- Daniel Roe (Thu May 30 2019 - 18:29:13 PDT)
- Reber, David (Thu May 30 2019 - 18:23:39 PDT)
- Daniel Roe (Thu May 30 2019 - 18:15:29 PDT)
- Reber, David (Thu May 30 2019 - 17:31:45 PDT)
- Daniel Roe (Thu May 30 2019 - 08:03:21 PDT)
- Reber, David (Wed May 29 2019 - 20:24:20 PDT)
[AMBER] Random segfaults (invalid memory reference) in sander
- Daniel Roe (Wed May 15 2019 - 08:52:10 PDT)
- Charo del Genio (Wed May 15 2019 - 08:45:27 PDT)
- David A Case (Mon May 06 2019 - 07:52:18 PDT)
- Charo del Genio (Mon May 06 2019 - 02:37:34 PDT)
- scanya.interia.eu (Fri May 03 2019 - 07:23:10 PDT)
- Charo del Genio (Fri May 03 2019 - 07:08:31 PDT)
- Daniel Roe (Fri May 03 2019 - 05:29:15 PDT)
- Daniel Roe (Fri May 03 2019 - 05:27:15 PDT)
- Margarita I. Bernal-Uruchurtu (Fri May 03 2019 - 02:11:59 PDT)
- Charo del Genio (Thu May 02 2019 - 10:51:31 PDT)
- James Kress (Thu May 02 2019 - 10:28:48 PDT)
- Charo del Genio (Thu May 02 2019 - 01:43:19 PDT)
[AMBER] reduce info.log
- Sadaf Rani (Wed May 29 2019 - 03:08:02 PDT)
- David A Case (Tue May 28 2019 - 10:35:07 PDT)
- Sadaf Rani (Tue May 28 2019 - 04:38:07 PDT)
[AMBER] Regarding building of parallel version of AMBER18 in centos 7
- Rajarshi Roy (Thu May 23 2019 - 06:40:42 PDT)
- David A Case (Wed May 22 2019 - 05:03:30 PDT)
- Rajarshi Roy (Tue May 21 2019 - 20:49:41 PDT)
[AMBER] Regarding GTX 1050 Ti
- Rajarshi Roy (Sat May 11 2019 - 11:51:28 PDT)
- Ross Walker (Sat May 11 2019 - 11:23:40 PDT)
- Rajarshi Roy (Fri May 10 2019 - 20:22:09 PDT)
[AMBER] Releasing SIRAH lipids! A complete coarse-grained force field running on AMBER
- Matias Machado (Wed May 15 2019 - 11:30:57 PDT)
[AMBER] Residence time around ions
- Reber, David (Sun May 12 2019 - 03:58:43 PDT)
[AMBER] rmsd
- David Case (Mon May 27 2019 - 18:49:22 PDT)
- Kenneth Huang (Mon May 27 2019 - 18:18:27 PDT)
- Hirdesh Kumar (Mon May 27 2019 - 11:35:16 PDT)
[AMBER] RMSF of combined trajectory
- Rinsha Chk (Sun May 19 2019 - 21:23:40 PDT)
- Daniel Roe (Fri May 17 2019 - 05:23:23 PDT)
- Rinsha Chk (Fri May 17 2019 - 00:08:53 PDT)
- Bill Ross (Thu May 16 2019 - 23:17:31 PDT)
- Bill Ross (Thu May 16 2019 - 23:16:02 PDT)
- Rinsha Chk (Thu May 16 2019 - 22:26:58 PDT)
- Bill Ross (Thu May 16 2019 - 04:59:21 PDT)
- Rinsha Chk (Thu May 16 2019 - 04:43:37 PDT)
[AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword]
- Erdem Yeler (Sun May 05 2019 - 04:30:44 PDT)
- Carlos Simmerling (Sun May 05 2019 - 03:57:32 PDT)
- Erdem Yeler (Sun May 05 2019 - 03:03:59 PDT)
- Carlos Simmerling (Sat May 04 2019 - 03:39:42 PDT)
- Erdem Yeler (Sat May 04 2019 - 02:57:44 PDT)
- Erdem Yeler (Sat May 04 2019 - 02:56:05 PDT)
- Kellon Belfon (Fri May 03 2019 - 08:49:00 PDT)
- Kellon Belfon (Fri May 03 2019 - 08:22:22 PDT)
- Erdem Yeler (Fri May 03 2019 - 02:36:48 PDT)
[AMBER] running qsub files in a single standalone workstation
- Nadine Homeyer (Tue May 07 2019 - 23:09:28 PDT)
- ali akbar (Tue May 07 2019 - 22:32:49 PDT)
- David A Case (Tue May 07 2019 - 04:16:58 PDT)
- ali akbar (Tue May 07 2019 - 03:28:21 PDT)
[AMBER] Selecting number of waters in tleap
- Kellon Belfon (Fri May 17 2019 - 11:07:00 PDT)
- Matias Machado (Fri May 17 2019 - 07:19:02 PDT)
- Elena Gomez (Fri May 17 2019 - 01:09:35 PDT)
[AMBER] set RA, RT and n_partition in adQM/MM run
- Ruth Helena Tichauer (Wed May 15 2019 - 03:57:38 PDT)
[AMBER] Simulating Water Exchange to Buried Binding Sites
- Charles Lin (Mon May 20 2019 - 10:10:56 PDT)
- Charles Lin (Mon May 20 2019 - 10:09:22 PDT)
- Matias Machado (Fri May 17 2019 - 11:22:10 PDT)
- Debarati DasGupta (Fri May 17 2019 - 11:18:09 PDT)
- Charles Lin (Fri May 17 2019 - 10:45:25 PDT)
- Matias Machado (Fri May 17 2019 - 07:14:06 PDT)
- Debarati DasGupta (Thu May 16 2019 - 06:21:44 PDT)
[AMBER] Simulation with Protein, cofactor and Ligand
- David A Case (Wed May 01 2019 - 10:53:53 PDT)
[AMBER] SIRAH force field goes quantum in AMBER
- Matias Machado (Fri May 03 2019 - 13:12:34 PDT)
[AMBER] SMD using contact number
- Feng Pan (Thu May 02 2019 - 08:50:29 PDT)
- Chem Jubilant (Wed May 01 2019 - 07:40:46 PDT)
[AMBER] Solute free non-water solvent
- David A Case (Tue May 14 2019 - 10:34:58 PDT)
- razie yousefi (Tue May 14 2019 - 08:01:17 PDT)
[AMBER] Some basic question
- David A Case (Tue May 28 2019 - 10:51:29 PDT)
- Sina (Fri May 24 2019 - 09:18:41 PDT)
[AMBER] SPAM bulk solvent free energy parameters
- Daniel Roe (Thu May 09 2019 - 11:39:26 PDT)
- Debarati DasGupta (Tue May 07 2019 - 06:36:51 PDT)
[AMBER] Suggestion about proper ANTECHAMBER usage
- Saikat Dutta chowdhury (Fri May 17 2019 - 06:54:27 PDT)
- David A Case (Fri May 17 2019 - 06:25:17 PDT)
- Saikat Dutta chowdhury (Fri May 17 2019 - 04:38:52 PDT)
[AMBER] Temperature variation in QM/MM simulation with AMBER18/G09
- Abhilash J (Fri May 24 2019 - 22:53:38 PDT)
- David A Case (Thu May 23 2019 - 06:00:40 PDT)
- Abhilash J (Wed May 22 2019 - 11:38:05 PDT)
[AMBER] Thermostat question
- Daniel Roe (Thu May 09 2019 - 11:21:10 PDT)
- Markowska (Wed May 08 2019 - 13:32:46 PDT)
- Daniel Roe (Wed May 08 2019 - 05:55:08 PDT)
- David Cerutti (Wed May 08 2019 - 00:22:16 PDT)
- Markowska (Tue May 07 2019 - 23:51:52 PDT)
[AMBER] three letter code for unprotonated carboxyglutamates
- Pietro Aronica (Tue May 07 2019 - 02:52:12 PDT)
- Tanusree S (Tue May 07 2019 - 02:45:25 PDT)
[AMBER] tleap split lipid when it shouldn't
- Maximilien BERNE (Mon May 20 2019 - 07:48:12 PDT)
- Sally Pias (Wed May 15 2019 - 15:12:15 PDT)
- Stephan Schott (Wed May 15 2019 - 10:42:50 PDT)
- Stephan Schott (Wed May 15 2019 - 10:35:22 PDT)
- Matias Machado (Wed May 15 2019 - 10:15:32 PDT)
- Maximilien BERNE (Wed May 15 2019 - 07:17:52 PDT)
- David A Case (Wed May 15 2019 - 06:08:40 PDT)
- Maximilien BERNE (Wed May 15 2019 - 03:18:29 PDT)
- Dickson, Callum (Mon May 13 2019 - 08:57:36 PDT)
- Maximilien BERNE (Mon May 13 2019 - 08:23:28 PDT)
- Dickson, Callum (Mon May 13 2019 - 07:49:49 PDT)
- Maximilien BERNE (Mon May 13 2019 - 07:37:09 PDT)
- Maximilien BERNE (Mon May 13 2019 - 07:32:03 PDT)
- Dickson, Callum (Mon May 13 2019 - 06:56:21 PDT)
- David A Case (Mon May 13 2019 - 06:50:41 PDT)
- Maximilien BERNE (Mon May 13 2019 - 05:41:42 PDT)
[AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016
- Pratul Agarwal (Tue May 14 2019 - 06:31:01 PDT)
- Akshay Prabhakant (Tue May 14 2019 - 03:03:12 PDT)
- Pratul Agarwal (Mon May 13 2019 - 07:24:10 PDT)
- Akshay Prabhakant (Mon May 13 2019 - 07:01:26 PDT)
- Akshay Prabhakant (Mon May 13 2019 - 06:53:49 PDT)
[AMBER] umbrella sampling using pmemd in amber/2016
- Feng Pan (Tue May 07 2019 - 09:26:58 PDT)
- Akshay Prabhakant (Sun May 05 2019 - 08:30:04 PDT)
[AMBER] Unequal distribution of water
- Carlos Simmerling (Tue May 07 2019 - 15:41:04 PDT)
- Piotr Fajer (Tue May 07 2019 - 14:26:29 PDT)
[AMBER] Using a box of organic solvent
- David A Case (Fri May 31 2019 - 05:14:51 PDT)
- Alessandro LANDI (Fri May 31 2019 - 03:42:08 PDT)
[AMBER] Velocity rescaling between different temperatures?
- Daniel Roe (Mon May 20 2019 - 09:33:25 PDT)
- Kenneth Huang (Mon May 20 2019 - 09:25:38 PDT)
- Daniel Roe (Mon May 20 2019 - 05:28:04 PDT)
- Kenneth Huang (Fri May 17 2019 - 12:18:15 PDT)
[AMBER] Vina Zinc
- Beale, John (Wed May 01 2019 - 04:05:56 PDT)
[AMBER] Volmap command in cpptraj followed by SPAM
- Debarati DasGupta (Thu May 23 2019 - 06:59:28 PDT)

Amber Archive May 2019 by subject