Amber Archive Jul 2025: by thread

Re: [AMBER] Instability when continuing GPU simulation with Berendsen Barostat on Cluster (A100) David A Case via AMBER (Tue Jul 01 2025 - 20:44:52 PDT)
- Re: [AMBER] Instability when continuing GPU simulation with Berendsen Barostat on Cluster (A100) Téletchéa Stéphane via AMBER (Wed Jul 02 2025 - 02:48:09 PDT)
[AMBER] Negative Temperature and SHAKE problems in MD with Frozen Atoms Matthew Tremblay via AMBER (Wed Jul 02 2025 - 08:20:07 PDT)
- Re: [AMBER] Negative Temperature and SHAKE problems in MD with Frozen Atoms David A Case via AMBER (Sun Jul 06 2025 - 11:10:28 PDT)
[AMBER] Difficulties? using GBNSR6 with MMPBSA.py Johann, Timothy via AMBER (Wed Jul 02 2025 - 11:12:14 PDT)
[AMBER] RNA G quadruplex simulation with ions Debarati DasGupta via AMBER (Wed Jul 02 2025 - 12:41:13 PDT)
- Re: [AMBER] RNA G quadruplex simulation with ions Christina Bergonzo via AMBER (Thu Jul 03 2025 - 06:35:57 PDT)
[AMBER] Query regarding Installation of VFFDT on Linux via Wine Arka Acharyya via AMBER (Thu Jul 03 2025 - 08:19:02 PDT)
Re: [AMBER] Building double bilayer using packmol-memgen Cherry, Kendall via AMBER (Thu Jul 03 2025 - 13:01:16 PDT)
[AMBER] To select the closest ions MAMTA YADAV via AMBER (Sat Jul 05 2025 - 03:33:04 PDT)
- Re: [AMBER] To select the closest ions David A Case via AMBER (Sun Jul 06 2025 - 11:14:11 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] How to generate force field parameters for boron containing compound using paramfit Arka Acharyya via AMBER (Mon Jul 07 2025 - 07:10:07 PDT)
- Re: [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)
[AMBER] Berendsen Barostat Underestimates Density in QM/MM Zihao Bai via AMBER (Mon Jul 07 2025 - 11:32:31 PDT)
[AMBER] Adapting angle parameters for new angles Christian Seitz via AMBER (Mon Jul 07 2025 - 13:27:22 PDT)
- Re: [AMBER] Adapting angle parameters for new angles Timothy Giese via AMBER (Mon Jul 07 2025 - 14:07:57 PDT)
  - Re: [AMBER] Adapting angle parameters for new angles Christian Seitz via AMBER (Tue Jul 08 2025 - 12:00:10 PDT)
Re: [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] Amber fails to compile with boost-1.88 Charo del Genio via AMBER (Tue Jul 08 2025 - 03:17:27 PDT)
[AMBER] Constant force Molecular Dynamics Simulation MAMTA YADAV via AMBER (Fri Jul 11 2025 - 12:33:50 PDT)
- Re: [AMBER] Constant force Molecular Dynamics Simulation David A Case via AMBER (Sun Jul 13 2025 - 07:56:01 PDT)
- Re: [AMBER] Constant force Molecular Dynamics Simulation Daniel Roe via AMBER (Sun Jul 13 2025 - 09:40:48 PDT)
[AMBER] Adaptively Biased MD (abmd) Dulal Mondal via AMBER (Sat Jul 12 2025 - 07:22:21 PDT)
- Re: [AMBER] Adaptively Biased MD (abmd) Feng Pan via AMBER (Sat Jul 12 2025 - 22:07:04 PDT)
  - Re: [AMBER] Adaptively Biased MD (abmd) Dulal Mondal via AMBER (Sun Jul 13 2025 - 21:34:32 PDT)
    - Re: [AMBER] Adaptively Biased MD (abmd) Dulal Mondal via AMBER (Tue Jul 15 2025 - 05:58:55 PDT)
[AMBER] Amber ForceField Parameter for Boron atom Arka Acharyya via AMBER (Sat Jul 12 2025 - 23:27:11 PDT)
- Re: [AMBER] Amber ForceField Parameter for Boron atom David A Case via AMBER (Sun Jul 13 2025 - 08:10:15 PDT)
[AMBER] How to set AMBERHOME with v25 Charles-Alexandre Mattelaer via AMBER (Sun Jul 13 2025 - 05:43:19 PDT)
[AMBER] MMPBSA Ven, Wouter van de via AMBER (Mon Jul 14 2025 - 02:05:55 PDT)
- Re: [AMBER] MMPBSA Elvis Martis via AMBER (Mon Jul 14 2025 - 03:29:47 PDT)
- Re: [AMBER] MMPBSA Elvis Martis via AMBER (Mon Jul 14 2025 - 05:15:47 PDT)
[AMBER] Force field parameters for Xenon Carmen Al Masri Said via AMBER (Mon Jul 14 2025 - 09:42:57 PDT)
[AMBER] Choice of protein/water force fields with ZAFF zinc parameters? Cherry, Kendall via AMBER (Mon Jul 14 2025 - 12:25:54 PDT)
- Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? Cherry, Kendall via AMBER (Mon Jul 14 2025 - 12:29:40 PDT)
  - Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? Li, Zhen via AMBER (Mon Jul 14 2025 - 15:33:43 PDT)
    - Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? Cherry, Kendall via AMBER (Mon Jul 14 2025 - 16:57:13 PDT)
    - Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? Li, Zhen via AMBER (Tue Jul 15 2025 - 02:35:32 PDT)
    - Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? Cherry, Kendall via AMBER (Tue Jul 15 2025 - 04:36:31 PDT)
[AMBER] pmemd24 problems with RTX5090 Oscar Conchillo-Solé via AMBER (Tue Jul 15 2025 - 00:48:54 PDT)
- Re: [AMBER] pmemd24 problems with RTX5090 David A Case via AMBER (Tue Jul 15 2025 - 10:44:12 PDT)
- Re: [AMBER] pmemd24 problems with RTX5090 David A Case via AMBER (Wed Jul 16 2025 - 07:32:57 PDT)
[AMBER] pmemd.cuda in Amber24 is failing all test (RTX 5090 + CUDA 12.9) Biplab Ghosh via AMBER (Wed Jul 16 2025 - 05:05:32 PDT)
- Re: [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)
[AMBER] Announcement: Release of DOCK 6.13 Scott Brozell via AMBER (Wed Jul 16 2025 - 14:33:54 PDT)
[AMBER] How are the A and B coefficients for LJ parameters determined? Markowska (Thu Jul 17 2025 - 03:22:21 PDT)
- Re: [AMBER] How are the A and B coefficients for LJ parameters determined? Markowska (Thu Jul 17 2025 - 05:42:04 PDT)
- Re: [AMBER] How are the A and B coefficients for LJ parameters determined? Markowska (Thu Jul 17 2025 - 06:11:42 PDT)
[AMBER] Negative Temperature Bug with Belly Dynamics Matthew Tremblay via AMBER (Thu Jul 17 2025 - 11:52:43 PDT)
[AMBER] Problems in installing AmberTools25 Simona Saporiti via AMBER (Fri Jul 18 2025 - 01:55:07 PDT)
- Re: [AMBER] Problems in installing AmberTools25 Li, Zhen via AMBER (Fri Jul 18 2025 - 03:37:19 PDT)
[AMBER] Differences in Umbrella Sampling between Amber18 and Amber24 Aadarsh Raghunathan via AMBER (Sat Jul 19 2025 - 09:57:28 PDT)
- Re: [AMBER] Differences in Umbrella Sampling between Amber18 and Amber24 Sidharth E K via AMBER (Mon Jul 21 2025 - 22:26:32 PDT)
[AMBER] MMPBSA.py results unresponsive to changes in epsin Johann, Timothy via AMBER (Mon Jul 21 2025 - 14:16:04 PDT)
- [AMBER] MMPBSA.py results unresponsive to changes in epsin Johann, Timothy via AMBER (Mon Jul 21 2025 - 15:02:15 PDT)
  - Re: [AMBER] MMPBSA.py results unresponsive to changes in epsin Ray Luo via AMBER (Mon Jul 21 2025 - 16:25:46 PDT)
    - Re: [AMBER] MMPBSA.py results unresponsive to changes in epsin Johann, Timothy via AMBER (Mon Jul 21 2025 - 19:09:41 PDT)
    - Re: [AMBER] MMPBSA.py results unresponsive to changes in epsin David A Case via AMBER (Thu Jul 24 2025 - 07:31:33 PDT)
Re: [AMBER] AMBER Digest, Vol 4760, Issue 1 Kriti Shukla via AMBER (Mon Jul 21 2025 - 21:34:24 PDT)
[AMBER] different memory usage by Amber16 and Amber24 Umut Çağan Uçar via AMBER (Wed Jul 23 2025 - 19:03:28 PDT)
- Re: [AMBER] different memory usage by Amber16 and Amber24 David A Case via AMBER (Thu Jul 24 2025 - 07:35:59 PDT)
[AMBER] MD simulations running slowly Lucas Gasparello Viviani via AMBER (Thu Jul 24 2025 - 08:52:30 PDT)
[AMBER] Problems with MMPB/MMGBSA Johnny Su via AMBER (Sun Jul 27 2025 - 03:06:29 PDT)
- [AMBER] CIF parsing needs to be updated Istvan Kolossvary via AMBER (Tue Jul 29 2025 - 11:40:55 PDT)
Re: [AMBER] To calculate the volume of an octahedral box Daniel Roe via AMBER (Thu Jul 31 2025 - 11:37:52 PDT)
[AMBER] Help with optimizing the time of calculation Lucas Gasparello Viviani via AMBER (Thu Jul 31 2025 - 14:02:50 PDT)

Amber Archive Jul 2025 by thread