Amber Archive May 2023: by subject

[AMBER] 1-4 scaling in GLYCAM
- Richard Kullmann via AMBER (Wed May 24 2023 - 05:20:03 PDT)
- David A Case via AMBER (Wed May 24 2023 - 04:55:55 PDT)
- Richard Kullmann via AMBER (Wed May 24 2023 - 02:25:06 PDT)
[AMBER] 247 tests experienced errors
- David A Case via AMBER (Fri May 19 2023 - 18:13:12 PDT)
- Pertschy, Florian via AMBER (Fri May 19 2023 - 07:38:24 PDT)
[AMBER] [Sender Not Verified] Are forcefields valid under high pressures
- Steinbrecher, Thomas via AMBER (Mon May 15 2023 - 00:19:01 PDT)
[AMBER] [Sender Not Verified] trajin and outtraj command
- Daniel Roe via AMBER (Thu May 18 2023 - 08:20:21 PDT)
- Daniel Roe via AMBER (Thu May 18 2023 - 08:19:32 PDT)
- Steinbrecher, Thomas via AMBER (Tue May 09 2023 - 23:30:50 PDT)
[AMBER] Amber 2020 Installation issues on Mac OS Ventura
- Scott Brozell via AMBER (Tue May 02 2023 - 14:26:39 PDT)
- Markus Metz via AMBER (Tue May 02 2023 - 12:05:35 PDT)
[AMBER] amber 22 and ubuntu 22
- Sepideh Jafari via AMBER (Tue May 23 2023 - 06:34:46 PDT)
[AMBER] Amber cannot find blas from cray-libsci
- David A Case via AMBER (Thu May 11 2023 - 09:17:57 PDT)
- Siwakorn Sukharom via AMBER (Wed May 10 2023 - 23:21:31 PDT)
[AMBER] Amber20 installation Error
- angad sharma via AMBER (Tue May 02 2023 - 05:12:05 PDT)
[AMBER] Amber22 Could not import mpi4py package.
- Siwakorn Sukharom via AMBER (Mon May 15 2023 - 19:08:23 PDT)
- Martin Juhás via AMBER (Mon May 15 2023 - 06:31:04 PDT)
- Siwakorn Sukharom via AMBER (Sun May 14 2023 - 23:20:06 PDT)
[AMBER] Amber22 CUDA compilation problem
- Irek Porebski via AMBER (Tue May 30 2023 - 18:40:44 PDT)
- Pertschy, Florian via AMBER (Tue May 30 2023 - 13:42:40 PDT)
- Irek Porebski via AMBER (Tue May 30 2023 - 06:06:01 PDT)
[AMBER] AMBERTools23 AMBER22 ReaxFF Install
- Rudy Richardson via AMBER (Mon May 01 2023 - 05:51:37 PDT)
[AMBER] AmberTools23 fails to build with python 3.11
- Charo del Genio via AMBER (Wed May 03 2023 - 13:59:21 PDT)
[AMBER] Are forcefields valid under high pressures
- Matthew Guberman-Pfeffer via AMBER (Fri May 12 2023 - 12:56:04 PDT)
[AMBER] Bug in PBSA with torch (patch included)
- Charo del Genio via AMBER (Thu May 04 2023 - 03:16:45 PDT)
[AMBER] Calculate min distance between periodic images
- Hocine EL KHAOUDI ENYOURY via AMBER (Mon May 29 2023 - 06:54:37 PDT)
[AMBER] Calculating diffusion constant for NPT trajectories with CPPTRAJ
- Daniel Roe via AMBER (Fri May 12 2023 - 12:38:35 PDT)
[AMBER] Can pmemd.cuda.MPI run on gpu with compute mode set as exclusive process?
- Ross Walker via AMBER (Wed May 10 2023 - 04:35:38 PDT)
- Siwakorn Sukharom via AMBER (Wed May 10 2023 - 01:44:34 PDT)
[AMBER] Cluster size
- Daniel Roe via AMBER (Thu May 18 2023 - 08:03:08 PDT)
- Daniel Hall via AMBER (Mon May 15 2023 - 07:42:50 PDT)
[AMBER] Cluster size from independent trajectories.
- Daniel Hall via AMBER (Tue May 02 2023 - 03:02:40 PDT)
[AMBER] compiling amber 22 with gcc 11 / cuda 11.6: cuda error with mdgx
- David A Case via AMBER (Tue May 09 2023 - 11:11:13 PDT)
[AMBER] Constant pH
- Hoang, Oanh Tu via AMBER (Wed May 10 2023 - 02:01:06 PDT)
[AMBER] Convertion of .mdvel to .veldcd
- Daniel Roe via AMBER (Tue May 09 2023 - 12:43:57 PDT)
- Daniel Roe via AMBER (Tue May 09 2023 - 06:26:50 PDT)
- Shakuntala Dhurua via AMBER (Tue May 09 2023 - 05:29:52 PDT)
[AMBER] counting waters in a buried cavity
- Markowska (Tue May 09 2023 - 06:07:23 PDT)
- Patricio German Barletta via AMBER (Tue May 09 2023 - 01:15:08 PDT)
- Marion Silvestrini via AMBER (Mon May 08 2023 - 09:56:13 PDT)
[AMBER] CpHMD simulation run
- David A Case via AMBER (Tue May 09 2023 - 11:04:50 PDT)
- Dulal Mondal via AMBER (Mon May 08 2023 - 23:56:48 PDT)
[AMBER] CpHMD, advice
- Matthew Guberman-Pfeffer via AMBER (Tue May 09 2023 - 06:07:16 PDT)
[AMBER] CPPTRAJ, FixAtomOrder peculiarity
- Daniel Roe via AMBER (Tue May 30 2023 - 11:08:35 PDT)
- Matthew Guberman-Pfeffer via AMBER (Fri May 26 2023 - 09:26:14 PDT)
[AMBER] Cuda accelerated GIST-PME?
- Franz Waibl via AMBER (Sun May 07 2023 - 03:36:02 PDT)
- Brian Radak via AMBER (Fri May 05 2023 - 10:29:54 PDT)
[AMBER] Does amber 22 work on Ubuntu 22.04
- Martin Juhás via AMBER (Tue May 16 2023 - 23:37:15 PDT)
- Ming Tang via AMBER (Tue May 16 2023 - 19:10:55 PDT)
[AMBER] FATAL: Atom .R<NME 42>.A<CH3 7> does not have a type in tleap
- Carlos Simmerling via AMBER (Wed May 03 2023 - 12:10:39 PDT)
- Debarati DasGupta via AMBER (Wed May 03 2023 - 11:59:25 PDT)
[AMBER] Fwd: Residence time and/or survival probability of water using cpptraj
- Dulal Mondal via AMBER (Thu May 04 2023 - 22:03:46 PDT)
[AMBER] GAMD/TI issue in Ambaer20/22
- mish via AMBER (Wed May 24 2023 - 15:36:08 PDT)
- mish via AMBER (Wed May 24 2023 - 14:54:08 PDT)
- mish via AMBER (Wed May 24 2023 - 10:35:48 PDT)
- mish via AMBER (Tue May 23 2023 - 12:59:01 PDT)
[AMBER] GPUs for ABFE
- Nikolay N. Kuzmich via AMBER (Tue May 09 2023 - 12:13:09 PDT)
[AMBER] How to convert amber trajectory to .tpr file in gromacs format
- Daniel Roe via AMBER (Wed May 17 2023 - 08:57:15 PDT)
- SANKAR MAITY via AMBER (Tue May 16 2023 - 22:05:45 PDT)
[AMBER] inf pKa values constant pH
- Vinicius Wilian Cruzeiro via AMBER (Wed May 24 2023 - 20:27:19 PDT)
- Hoang, Oanh Tu via AMBER (Wed May 24 2023 - 02:42:13 PDT)
[AMBER] Insights for understanding the flags in input files
- Domenico Marson via AMBER (Fri May 05 2023 - 01:16:36 PDT)
- Priyasha Majee via AMBER (Thu May 04 2023 - 23:25:56 PDT)
[AMBER] Installation fails: libfftw3.a: relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
- Pertschy, Florian via AMBER (Tue May 30 2023 - 03:21:25 PDT)
[AMBER] Installing AmberTools23 with anaconda
- David A Case via AMBER (Sat May 06 2023 - 14:07:57 PDT)
- Lee, Chris via AMBER (Sat May 06 2023 - 09:52:31 PDT)
[AMBER] MCPB.py doesn't recognize a ligand.
- DE-SANTANA-PONTES, FREDERICO J. via AMBER (Mon May 22 2023 - 15:46:05 PDT)
[AMBER] MCPB.py RESP charge The number of the residue names given is mismatch the database
- DE-SANTANA-PONTES, FREDERICO J. via AMBER (Wed May 31 2023 - 11:30:58 PDT)
[AMBER] MCPB.py step 4n1 error
- Jasmin Güven via AMBER (Fri May 05 2023 - 05:13:59 PDT)
[AMBER] mdp parameters when using the AMBER force field with GROMACS
- Arun Srikanth via AMBER (Wed May 31 2023 - 10:00:30 PDT)
- Arun Srikanth via AMBER (Fri May 26 2023 - 10:47:11 PDT)
- Eduard Neu via AMBER (Fri May 26 2023 - 09:57:44 PDT)
[AMBER] Memory leak in amber22 pmemd.cuda
- Ross Walker via AMBER (Fri May 26 2023 - 10:35:15 PDT)
- 张志伟 via AMBER (Fri May 26 2023 - 08:46:13 PDT)
[AMBER] Merging two prmtop files
- Steinbrecher, Thomas via AMBER (Mon May 01 2023 - 23:41:29 PDT)
[AMBER] Missing atom types in parmchk.dat
- Robert Heße via AMBER (Thu May 25 2023 - 04:37:50 PDT)
- Robert Heße via AMBER (Thu May 25 2023 - 04:36:00 PDT)
- David A Case via AMBER (Tue May 23 2023 - 10:06:36 PDT)
- Rodrigo Galindo-Murillo via AMBER (Mon May 22 2023 - 09:18:25 PDT)
- Robert Heße via AMBER (Mon May 22 2023 - 07:37:50 PDT)
[AMBER] native contacts nucleic acid
- Prithviraj Nandigrami via AMBER (Fri May 12 2023 - 12:40:43 PDT)
- Prithviraj Nandigrami via AMBER (Wed May 10 2023 - 08:26:54 PDT)
[AMBER] Negative barrier term when fitting with mdgx
- He, Amy via AMBER (Wed May 31 2023 - 08:06:18 PDT)
- Rodrigo Galindo-Murillo via AMBER (Wed May 31 2023 - 07:59:40 PDT)
- Carlos Simmerling via AMBER (Wed May 31 2023 - 05:19:06 PDT)
- Robert Heße via AMBER (Wed May 31 2023 - 05:06:31 PDT)
[AMBER] NFE-Error ** : CV #1 (COM_DISTANCE) : too few integers
- mish via AMBER (Wed May 10 2023 - 11:53:09 PDT)
- mish via AMBER (Wed May 10 2023 - 11:27:06 PDT)
[AMBER] No time information in cpout file
- Dulal Mondal via AMBER (Mon May 08 2023 - 20:25:58 PDT)
[AMBER] ntf for LiGaMD in Amber20/22
- mish via AMBER (Wed May 17 2023 - 14:24:23 PDT)
[AMBER] on-going issues installing amber on mint
- David A Case via AMBER (Thu May 18 2023 - 08:58:46 PDT)
- nahoum a via AMBER (Tue May 16 2023 - 03:14:17 PDT)
[AMBER] OPC3-pol
- Piia Bartos via AMBER (Mon May 22 2023 - 23:03:49 PDT)
- Piia Bartos via AMBER (Mon May 22 2023 - 04:04:17 PDT)
- Yeyue Xiong via AMBER (Fri May 19 2023 - 17:36:13 PDT)
[AMBER] Pairwise non-bonded interaction energy calculation
- Daniel Roe via AMBER (Wed May 10 2023 - 17:44:11 PDT)
- ChenXin via AMBER (Tue May 09 2023 - 06:21:46 PDT)
[AMBER] Parametrizing Pt(II) complex with MCPB.py
- Maciej Spiegel via AMBER (Wed May 31 2023 - 08:45:40 PDT)
- Maciej Spiegel via AMBER (Wed May 31 2023 - 08:41:19 PDT)
[AMBER] Periodic box
- yunshi11 via AMBER (Wed May 10 2023 - 15:25:40 PDT)
[AMBER] pmemd simulation exits abnormally
- mish via AMBER (Mon May 15 2023 - 09:37:49 PDT)
- Dickson, Callum via AMBER (Mon May 15 2023 - 08:43:55 PDT)
- mish via AMBER (Mon May 15 2023 - 07:34:11 PDT)
- Steinbrecher, Thomas via AMBER (Mon May 15 2023 - 07:15:18 PDT)
- Steinbrecher, Thomas via AMBER (Mon May 15 2023 - 06:50:43 PDT)
- David A Case via AMBER (Mon May 15 2023 - 05:21:24 PDT)
- Ignacio J. General via AMBER (Mon May 15 2023 - 05:18:04 PDT)
- Steinbrecher, Thomas via AMBER (Mon May 15 2023 - 01:25:54 PDT)
[AMBER] Poor Performance of Thermodynamic Integration using pmemd.cuda
- Kevin Mei via AMBER (Thu May 11 2023 - 19:31:19 PDT)
- David A Case via AMBER (Thu May 11 2023 - 09:10:40 PDT)
- Kevin Mei via AMBER (Wed May 10 2023 - 20:15:15 PDT)
[AMBER] Possible Failure with Amber22 serial and cuda installation
- David A Case via AMBER (Sat May 06 2023 - 14:11:13 PDT)
- Francesco Trozzi via AMBER (Fri May 05 2023 - 12:50:29 PDT)
[AMBER] Problem with aMD tutorial
- Charo del Genio via AMBER (Thu May 11 2023 - 02:37:19 PDT)
- Charo del Genio via AMBER (Wed May 10 2023 - 23:08:07 PDT)
- Raghuvir Pissurlenkar via AMBER (Wed May 10 2023 - 14:38:45 PDT)
- David A Case via AMBER (Wed May 10 2023 - 12:19:23 PDT)
- Raghuvir Pissurlenkar via AMBER (Wed May 10 2023 - 10:03:19 PDT)
[AMBER] question for insight
- Suchetana Gupta via AMBER (Thu May 04 2023 - 21:56:16 PDT)
- Priyasha Majee via AMBER (Thu May 04 2023 - 21:50:28 PDT)
[AMBER] question on minimization
- Suchetana Gupta via AMBER (Thu May 04 2023 - 21:29:09 PDT)
- Priyasha Majee via AMBER (Thu May 04 2023 - 21:26:22 PDT)
[AMBER] Residence time and/or survival probability of water using cpptraj
- Daniel Roe via AMBER (Wed May 10 2023 - 17:45:25 PDT)
- Daniel Roe via AMBER (Wed May 10 2023 - 17:41:54 PDT)
- Daniel Roe via AMBER (Fri May 05 2023 - 12:00:50 PDT)
- Dulal Mondal via AMBER (Wed May 03 2023 - 07:18:31 PDT)
[AMBER] Simple Amber GPU simulations on GridMarkets Cloud
- Ross Walker via AMBER (Mon May 22 2023 - 06:16:13 PDT)
[AMBER] Specifications of the QMMM coupling scheme in sander module?
- Alan Chien via AMBER (Wed May 24 2023 - 10:28:07 PDT)
- David A Case via AMBER (Wed May 24 2023 - 06:44:53 PDT)
- David A Case via AMBER (Wed May 24 2023 - 04:42:54 PDT)
- Alan Chien via AMBER (Tue May 23 2023 - 10:45:34 PDT)
[AMBER] trajin and outtraj command
- Dulal Mondal via AMBER (Tue May 09 2023 - 23:20:58 PDT)
[AMBER] Upload PyRED generated MOL2 file to CHARMM-GUI
- Eduard Neu via AMBER (Sun May 21 2023 - 06:50:12 PDT)
[AMBER] Velocities comparison to MB distribution
- Carlos Simmerling via AMBER (Sat May 27 2023 - 06:56:21 PDT)
- Martin Juhás via AMBER (Sat May 27 2023 - 05:47:51 PDT)
- Martin Juhás via AMBER (Wed May 24 2023 - 00:06:12 PDT)
[AMBER] where to download AmberTools21.tar.gz2
- David A Case via AMBER (Thu May 25 2023 - 05:24:54 PDT)
- 鱼翔 via AMBER (Wed May 24 2023 - 20:35:25 PDT)
- David A Case via AMBER (Wed May 24 2023 - 04:48:27 PDT)
- 鱼翔 via AMBER (Wed May 24 2023 - 00:10:11 PDT)

Amber Archive May 2023 by subject