Amber Archive Jul 2025: by subject

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

Amber Archive Jul 2025 by subject