Amber Archive Jul 2025 by author

67 messages: Starting Tue Jul 01 2025 - 21:00:02 PDT, Ending Thu Jul 31 2025 - 14:30:02 PDT
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Aadarsh Raghunathan via AMBER
- [AMBER] Differences in Umbrella Sampling between Amber18 and Amber24 (Sat Jul 19 2025 - 09:57:28 PDT)
Arka Acharyya via AMBER
- [AMBER] Amber ForceField Parameter for Boron atom (Sat Jul 12 2025 - 23:27:11 PDT)
- [AMBER] How to generate force field parameters for boron containing compound using paramfit (Mon Jul 07 2025 - 07:10:07 PDT)
- [AMBER] Query regarding Installation of VFFDT on Linux via Wine (Thu Jul 03 2025 - 08:19:02 PDT)
Biplab Ghosh via AMBER
- Re: [AMBER] pmemd.cuda in Amber24 is failing all test (RTX 5090 + CUDA 12.9) (Fri Jul 18 2025 - 07:31:44 PDT)
- [AMBER] pmemd.cuda in Amber24 is failing all test (RTX 5090 + CUDA 12.9) (Wed Jul 16 2025 - 05:05:32 PDT)
Carlos Simmerling via AMBER
- Re: [AMBER] How to generate force field parameters for boron containing compound using paramfit (Mon Jul 07 2025 - 07:22:15 PDT)
Carmen Al Masri Said via AMBER
- [AMBER] Force field parameters for Xenon (Mon Jul 14 2025 - 09:42:57 PDT)
Charles-Alexandre Mattelaer via AMBER
- [AMBER] How to set AMBERHOME with v25 (Sun Jul 13 2025 - 05:43:19 PDT)
Charo del Genio via AMBER
- [AMBER] Amber fails to compile with boost-1.88 (Tue Jul 08 2025 - 03:17:27 PDT)
Cherry, Kendall via AMBER
- Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? (Tue Jul 15 2025 - 04:36:31 PDT)
- Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? (Mon Jul 14 2025 - 16:57:13 PDT)
- [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? (Mon Jul 14 2025 - 12:25:54 PDT)
- Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? (Mon Jul 14 2025 - 12:29:40 PDT)
- Re: [AMBER] Building double bilayer using packmol-memgen (Thu Jul 03 2025 - 13:01:16 PDT)
Christian Seitz via AMBER
- Re: [AMBER] Adapting angle parameters for new angles (Tue Jul 08 2025 - 12:00:10 PDT)
- [AMBER] Adapting angle parameters for new angles (Mon Jul 07 2025 - 13:27:22 PDT)
Christina Bergonzo via AMBER
- Re: [AMBER] RNA G quadruplex simulation with ions (Thu Jul 03 2025 - 06:35:57 PDT)
Daniel Roe via AMBER
- Re: [AMBER] To calculate the volume of an octahedral box (Thu Jul 31 2025 - 11:37:52 PDT)
- Re: [AMBER] Constant force Molecular Dynamics Simulation (Sun Jul 13 2025 - 09:40:48 PDT)
David A Case via AMBER
- Re: [AMBER] different memory usage by Amber16 and Amber24 (Thu Jul 24 2025 - 07:35:59 PDT)
- Re: [AMBER] MMPBSA.py results unresponsive to changes in epsin (Thu Jul 24 2025 - 07:31:33 PDT)
- Re: [AMBER] pmemd24 problems with RTX5090 (Wed Jul 16 2025 - 07:32:57 PDT)
- Re: [AMBER] pmemd24 problems with RTX5090 (Tue Jul 15 2025 - 10:44:12 PDT)
- Re: [AMBER] Amber ForceField Parameter for Boron atom (Sun Jul 13 2025 - 08:10:15 PDT)
- Re: [AMBER] Constant force Molecular Dynamics Simulation (Sun Jul 13 2025 - 07:56:01 PDT)
- Re: [AMBER] Potential Bug in QM/MM Virial Calculation and Suggestions for Ewald Error Estimation in AMBER (Mon Jul 07 2025 - 14:36:22 PDT)
- Re: [AMBER] To select the closest ions (Sun Jul 06 2025 - 11:14:11 PDT)
- Re: [AMBER] Negative Temperature and SHAKE problems in MD with Frozen Atoms (Sun Jul 06 2025 - 11:10:28 PDT)
- Re: [AMBER] Instability when continuing GPU simulation with Berendsen Barostat on Cluster (A100) (Tue Jul 01 2025 - 20:44:52 PDT)
Debarati DasGupta via AMBER
- [AMBER] RNA G quadruplex simulation with ions (Wed Jul 02 2025 - 12:41:13 PDT)
Dulal Mondal via AMBER
- Re: [AMBER] Adaptively Biased MD (abmd) (Tue Jul 15 2025 - 05:58:55 PDT)
- Re: [AMBER] Adaptively Biased MD (abmd) (Sun Jul 13 2025 - 21:34:32 PDT)
- [AMBER] Adaptively Biased MD (abmd) (Sat Jul 12 2025 - 07:22:21 PDT)
Elvis Martis via AMBER
- Re: [AMBER] MMPBSA (Mon Jul 14 2025 - 05:15:47 PDT)
- Re: [AMBER] MMPBSA (Mon Jul 14 2025 - 03:29:47 PDT)
Feng Pan via AMBER
- Re: [AMBER] Adaptively Biased MD (abmd) (Sat Jul 12 2025 - 22:07:04 PDT)
Istvan Kolossvary via AMBER
- [AMBER] CIF parsing needs to be updated (Tue Jul 29 2025 - 11:40:55 PDT)
Johann, Timothy via AMBER
- Re: [AMBER] MMPBSA.py results unresponsive to changes in epsin (Mon Jul 21 2025 - 19:09:41 PDT)
- [AMBER] MMPBSA.py results unresponsive to changes in epsin (Mon Jul 21 2025 - 15:02:15 PDT)
- [AMBER] MMPBSA.py results unresponsive to changes in epsin (Mon Jul 21 2025 - 14:16:04 PDT)
- [AMBER] Difficulties? using GBNSR6 with MMPBSA.py (Wed Jul 02 2025 - 11:12:14 PDT)
Johnny Su via AMBER
- [AMBER] Problems with MMPB/MMGBSA (Sun Jul 27 2025 - 03:06:29 PDT)
Kriti Shukla via AMBER
- Re: [AMBER] AMBER Digest, Vol 4760, Issue 1 (Mon Jul 21 2025 - 21:34:24 PDT)
Li, Zhen via AMBER
- Re: [AMBER] Problems in installing AmberTools25 (Fri Jul 18 2025 - 03:37:19 PDT)
- Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? (Tue Jul 15 2025 - 02:35:32 PDT)
- Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? (Mon Jul 14 2025 - 15:33:43 PDT)
Lucas Gasparello Viviani via AMBER
- [AMBER] Help with optimizing the time of calculation (Thu Jul 31 2025 - 14:02:50 PDT)
- [AMBER] MD simulations running slowly (Thu Jul 24 2025 - 08:52:30 PDT)
MAMTA YADAV via AMBER
- [AMBER] Constant force Molecular Dynamics Simulation (Fri Jul 11 2025 - 12:33:50 PDT)
- [AMBER] To select the closest ions (Sat Jul 05 2025 - 03:33:04 PDT)
Markowska
- Re: [AMBER] How are the A and B coefficients for LJ parameters determined? (Thu Jul 17 2025 - 06:11:42 PDT)
- Re: [AMBER] How are the A and B coefficients for LJ parameters determined? (Thu Jul 17 2025 - 05:42:04 PDT)
- [AMBER] How are the A and B coefficients for LJ parameters determined? (Thu Jul 17 2025 - 03:22:21 PDT)
Matthew Tremblay via AMBER
- [AMBER] Negative Temperature Bug with Belly Dynamics (Thu Jul 17 2025 - 11:52:43 PDT)
- [AMBER] Negative Temperature and SHAKE problems in MD with Frozen Atoms (Wed Jul 02 2025 - 08:20:07 PDT)
Oscar Conchillo-Solé via AMBER
- [AMBER] pmemd24 problems with RTX5090 (Tue Jul 15 2025 - 00:48:54 PDT)
Rahul Singal via AMBER
- [AMBER] Help with MPI error: “MPI size is not a multiple of -ng” on ADA cluster (Amber24, T-REMD) (Sat Jul 05 2025 - 04:44:56 PDT)
Ray Luo via AMBER
- Re: [AMBER] MMPBSA.py results unresponsive to changes in epsin (Mon Jul 21 2025 - 16:25:46 PDT)
Scott Brozell via AMBER
- [AMBER] Announcement: Release of DOCK 6.13 (Wed Jul 16 2025 - 14:33:54 PDT)
Sidharth E K via AMBER
- Re: [AMBER] Differences in Umbrella Sampling between Amber18 and Amber24 (Mon Jul 21 2025 - 22:26:32 PDT)
Simona Saporiti via AMBER
- [AMBER] Problems in installing AmberTools25 (Fri Jul 18 2025 - 01:55:07 PDT)
Timothy Giese via AMBER
- Re: [AMBER] Adapting angle parameters for new angles (Mon Jul 07 2025 - 14:07:57 PDT)
Téletchéa Stéphane via AMBER
- Re: [AMBER] Instability when continuing GPU simulation with Berendsen Barostat on Cluster (A100) (Wed Jul 02 2025 - 02:48:09 PDT)
Umut Çağan Uçar via AMBER
- [AMBER] different memory usage by Amber16 and Amber24 (Wed Jul 23 2025 - 19:03:28 PDT)
Ven, Wouter van de via AMBER
- [AMBER] MMPBSA (Mon Jul 14 2025 - 02:05:55 PDT)
Zihao Bai via AMBER
- [AMBER] Berendsen Barostat Underestimates Density in QM/MM (Mon Jul 07 2025 - 11:32:31 PDT)