Amber Archive May 2023 by thread
- [AMBER] AMBERTools23 AMBER22 ReaxFF Install Rudy Richardson via AMBER (Mon May 01 2023 - 05:51:37 PDT)
- [AMBER] Merging two prmtop files Steinbrecher, Thomas via AMBER (Mon May 01 2023 - 23:41:29 PDT)
- [AMBER] Cluster size from independent trajectories. Daniel Hall via AMBER (Tue May 02 2023 - 03:02:40 PDT)
- [AMBER] Amber20 installation Error angad sharma via AMBER (Tue May 02 2023 - 05:12:05 PDT)
- [AMBER] Amber 2020 Installation issues on Mac OS Ventura Markus Metz via AMBER (Tue May 02 2023 - 12:05:35 PDT)
- [AMBER] Residence time and/or survival probability of water using cpptraj Dulal Mondal via AMBER (Wed May 03 2023 - 07:18:31 PDT)
- [AMBER] FATAL: Atom .R<NME 42>.A<CH3 7> does not have a type in tleap Debarati DasGupta via AMBER (Wed May 03 2023 - 11:59:25 PDT)
- [AMBER] AmberTools23 fails to build with python 3.11 Charo del Genio via AMBER (Wed May 03 2023 - 13:59:21 PDT)
- [AMBER] Bug in PBSA with torch (patch included) Charo del Genio via AMBER (Thu May 04 2023 - 03:16:45 PDT)
- [AMBER] question on minimization Priyasha Majee via AMBER (Thu May 04 2023 - 21:26:22 PDT)
- [AMBER] question for insight Priyasha Majee via AMBER (Thu May 04 2023 - 21:50:28 PDT)
- [AMBER] Insights for understanding the flags in input files Priyasha Majee via AMBER (Thu May 04 2023 - 23:25:56 PDT)
- [AMBER] MCPB.py step 4n1 error Jasmin Güven via AMBER (Fri May 05 2023 - 05:13:59 PDT)
- [AMBER] Cuda accelerated GIST-PME? Brian Radak via AMBER (Fri May 05 2023 - 10:29:54 PDT)
- [AMBER] Possible Failure with Amber22 serial and cuda installation Francesco Trozzi via AMBER (Fri May 05 2023 - 12:50:29 PDT)
- [AMBER] Installing AmberTools23 with anaconda Lee, Chris via AMBER (Sat May 06 2023 - 09:52:31 PDT)
- [AMBER] counting waters in a buried cavity Marion Silvestrini via AMBER (Mon May 08 2023 - 09:56:13 PDT)
- [AMBER] No time information in cpout file Dulal Mondal via AMBER (Mon May 08 2023 - 20:25:58 PDT)
- [AMBER] CpHMD simulation run Dulal Mondal via AMBER (Mon May 08 2023 - 23:56:48 PDT)
- [AMBER] Convertion of .mdvel to .veldcd Shakuntala Dhurua via AMBER (Tue May 09 2023 - 05:29:52 PDT)
- [AMBER] CpHMD, advice Matthew Guberman-Pfeffer via AMBER (Tue May 09 2023 - 06:07:16 PDT)
- [AMBER] Pairwise non-bonded interaction energy calculation ChenXin via AMBER (Tue May 09 2023 - 06:21:46 PDT)
- Re: [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] GPUs for ABFE Nikolay N. Kuzmich via AMBER (Tue May 09 2023 - 12:13:09 PDT)
- [AMBER] trajin and outtraj command Dulal Mondal via AMBER (Tue May 09 2023 - 23:20:58 PDT)
- [AMBER] Can pmemd.cuda.MPI run on gpu with compute mode set as exclusive process? Siwakorn Sukharom via AMBER (Wed May 10 2023 - 01:44:34 PDT)
- [AMBER] Constant pH Hoang, Oanh Tu via AMBER (Wed May 10 2023 - 02:01:06 PDT)
- [AMBER] native contacts nucleic acid Prithviraj Nandigrami via AMBER (Wed May 10 2023 - 08:26:54 PDT)
- [AMBER] Problem with aMD tutorial Raghuvir Pissurlenkar via AMBER (Wed May 10 2023 - 10:03:19 PDT)
- [AMBER] NFE-Error ** : CV #1 (COM_DISTANCE) : too few integers mish via AMBER (Wed May 10 2023 - 11:27:06 PDT)
- [AMBER] Periodic box yunshi11 via AMBER (Wed May 10 2023 - 15:25:40 PDT)
- [AMBER] Poor Performance of Thermodynamic Integration using pmemd.cuda Kevin Mei via AMBER (Wed May 10 2023 - 20:15:15 PDT)
- [AMBER] Amber cannot find blas from cray-libsci Siwakorn Sukharom via AMBER (Wed May 10 2023 - 23:21:31 PDT)
- [AMBER] Calculating diffusion constant for NPT trajectories with CPPTRAJ Daniel Roe via AMBER (Fri May 12 2023 - 12:38:35 PDT)
- [AMBER] Are forcefields valid under high pressures Matthew Guberman-Pfeffer via AMBER (Fri May 12 2023 - 12:56:04 PDT)
- [AMBER] Amber22 Could not import mpi4py package. Siwakorn Sukharom via AMBER (Sun May 14 2023 - 23:20:06 PDT)
- [AMBER] pmemd simulation exits abnormally Steinbrecher, Thomas via AMBER (Mon May 15 2023 - 01:25:54 PDT)
- [AMBER] Cluster size Daniel Hall via AMBER (Mon May 15 2023 - 07:42:50 PDT)
- [AMBER] on-going issues installing amber on mint nahoum a via AMBER (Tue May 16 2023 - 03:14:17 PDT)
- [AMBER] Does amber 22 work on Ubuntu 22.04 Ming Tang via AMBER (Tue May 16 2023 - 19:10:55 PDT)
- [AMBER] How to convert amber trajectory to .tpr file in gromacs format SANKAR MAITY via AMBER (Tue May 16 2023 - 22:05:45 PDT)
- [AMBER] ntf for LiGaMD in Amber20/22 mish via AMBER (Wed May 17 2023 - 14:24:23 PDT)
- [AMBER] 247 tests experienced errors Pertschy, Florian via AMBER (Fri May 19 2023 - 07:38:24 PDT)
- Re: [AMBER] OPC3-pol Yeyue Xiong via AMBER (Fri May 19 2023 - 17:36:13 PDT)
- [AMBER] Upload PyRED generated MOL2 file to CHARMM-GUI Eduard Neu via AMBER (Sun May 21 2023 - 06:50:12 PDT)
- [AMBER] Simple Amber GPU simulations on GridMarkets Cloud Ross Walker via AMBER (Mon May 22 2023 - 06:16:13 PDT)
- [AMBER] Missing atom types in parmchk.dat Robert Heße via AMBER (Mon May 22 2023 - 07:37:50 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] amber 22 and ubuntu 22 Sepideh Jafari via AMBER (Tue May 23 2023 - 06:34:46 PDT)
- [AMBER] Specifications of the QMMM coupling scheme in sander module? Alan Chien via AMBER (Tue May 23 2023 - 10:45:34 PDT)
- [AMBER] GAMD/TI issue in Ambaer20/22 mish via AMBER (Tue May 23 2023 - 12:59:01 PDT)
- [AMBER] Velocities comparison to MB distribution Martin Juhás via AMBER (Wed May 24 2023 - 00:06:12 PDT)
- [AMBER] where to download AmberTools21.tar.gz2 鱼翔 via AMBER (Wed May 24 2023 - 00:10:11 PDT)
- [AMBER] 1-4 scaling in GLYCAM Richard Kullmann via AMBER (Wed May 24 2023 - 02:25:06 PDT)
- [AMBER] inf pKa values constant pH Hoang, Oanh Tu via AMBER (Wed May 24 2023 - 02:42:13 PDT)
- [AMBER] Memory leak in amber22 pmemd.cuda 张志伟 via AMBER (Fri May 26 2023 - 08:46:13 PDT)
- [AMBER] CPPTRAJ, FixAtomOrder peculiarity Matthew Guberman-Pfeffer via AMBER (Fri May 26 2023 - 09:26:14 PDT)
- [AMBER] mdp parameters when using the AMBER force field with GROMACS Eduard Neu via AMBER (Fri May 26 2023 - 09:57:44 PDT)
- [AMBER] Calculate min distance between periodic images Hocine EL KHAOUDI ENYOURY via AMBER (Mon May 29 2023 - 06:54:37 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] Amber22 CUDA compilation problem Irek Porebski via AMBER (Tue May 30 2023 - 06:06:01 PDT)
- [AMBER] Negative barrier term when fitting with mdgx Robert Heße via AMBER (Wed May 31 2023 - 05:06:31 PDT)
- [AMBER] Parametrizing Pt(II) complex with MCPB.py Maciej Spiegel via AMBER (Wed May 31 2023 - 08:41:19 PDT)
- [AMBER] Parametrizing Pt(II) complex with MCPB.py Maciej Spiegel via AMBER (Wed May 31 2023 - 08:45:40 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)
- Last message date: Wed May 31 2023 - 12:00:02 PDT
- Archived on: Wed Dec 25 2024 - 05:56:15 PST
