Amber Archive Jul 2025 by date

67 messages: Starting Tue Jul 01 2025 - 21:00:02 PDT, Ending Thu Jul 31 2025 - 14:30:02 PDT
This period: Most recent messages
sort by: [ thread ] [ author ] [ date ] [ subject ] [ attachment ]

Tuesday, 1 July 2025
- Re: [AMBER] Instability when continuing GPU simulation with Berendsen Barostat on Cluster (A100) David A Case via AMBER
Wednesday, 2 July 2025
- Re: [AMBER] Instability when continuing GPU simulation with Berendsen Barostat on Cluster (A100) Téletchéa Stéphane via AMBER
- [AMBER] Negative Temperature and SHAKE problems in MD with Frozen Atoms Matthew Tremblay via AMBER
- [AMBER] Difficulties? using GBNSR6 with MMPBSA.py Johann, Timothy via AMBER
- [AMBER] RNA G quadruplex simulation with ions Debarati DasGupta via AMBER
Thursday, 3 July 2025
- Re: [AMBER] RNA G quadruplex simulation with ions Christina Bergonzo via AMBER
- [AMBER] Query regarding Installation of VFFDT on Linux via Wine Arka Acharyya via AMBER
- Re: [AMBER] Building double bilayer using packmol-memgen Cherry, Kendall via AMBER
Saturday, 5 July 2025
- [AMBER] To select the closest ions MAMTA YADAV via AMBER
- [AMBER] Help with MPI error: “MPI size is not a multiple of -ng” on ADA cluster (Amber24, T-REMD) Rahul Singal via AMBER
Sunday, 6 July 2025
- Re: [AMBER] Negative Temperature and SHAKE problems in MD with Frozen Atoms David A Case via AMBER
- Re: [AMBER] To select the closest ions David A Case via AMBER
Monday, 7 July 2025
- [AMBER] How to generate force field parameters for boron containing compound using paramfit Arka Acharyya via AMBER
- Re: [AMBER] How to generate force field parameters for boron containing compound using paramfit Carlos Simmerling via AMBER
- [AMBER] Berendsen Barostat Underestimates Density in QM/MM Zihao Bai via AMBER
- [AMBER] Adapting angle parameters for new angles Christian Seitz via AMBER
- Re: [AMBER] Adapting angle parameters for new angles Timothy Giese via AMBER
- Re: [AMBER] Potential Bug in QM/MM Virial Calculation and Suggestions for Ewald Error Estimation in AMBER David A Case via AMBER
Tuesday, 8 July 2025
- [AMBER] Amber fails to compile with boost-1.88 Charo del Genio via AMBER
- Re: [AMBER] Adapting angle parameters for new angles Christian Seitz via AMBER
Friday, 11 July 2025
- [AMBER] Constant force Molecular Dynamics Simulation MAMTA YADAV via AMBER
Saturday, 12 July 2025
- [AMBER] Adaptively Biased MD (abmd) Dulal Mondal via AMBER
- Re: [AMBER] Adaptively Biased MD (abmd) Feng Pan via AMBER
- [AMBER] Amber ForceField Parameter for Boron atom Arka Acharyya via AMBER
Sunday, 13 July 2025
- [AMBER] How to set AMBERHOME with v25 Charles-Alexandre Mattelaer via AMBER
- Re: [AMBER] Constant force Molecular Dynamics Simulation David A Case via AMBER
- Re: [AMBER] Amber ForceField Parameter for Boron atom David A Case via AMBER
- Re: [AMBER] Constant force Molecular Dynamics Simulation Daniel Roe via AMBER
- Re: [AMBER] Adaptively Biased MD (abmd) Dulal Mondal via AMBER
Monday, 14 July 2025
- [AMBER] MMPBSA Ven, Wouter van de via AMBER
- Re: [AMBER] MMPBSA Elvis Martis via AMBER
- Re: [AMBER] MMPBSA Elvis Martis via AMBER
- [AMBER] Force field parameters for Xenon Carmen Al Masri Said via AMBER
- Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? Cherry, Kendall via AMBER
- [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? Cherry, Kendall via AMBER
- Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? Li, Zhen via AMBER
- Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? Cherry, Kendall via AMBER
Tuesday, 15 July 2025
- [AMBER] pmemd24 problems with RTX5090 Oscar Conchillo-Solé via AMBER
- Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? Li, Zhen via AMBER
- Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? Cherry, Kendall via AMBER
- Re: [AMBER] Adaptively Biased MD (abmd) Dulal Mondal via AMBER
- Re: [AMBER] pmemd24 problems with RTX5090 David A Case via AMBER
Wednesday, 16 July 2025
- [AMBER] pmemd.cuda in Amber24 is failing all test (RTX 5090 + CUDA 12.9) Biplab Ghosh via AMBER
- Re: [AMBER] pmemd24 problems with RTX5090 David A Case via AMBER
- [AMBER] Announcement: Release of DOCK 6.13 Scott Brozell via AMBER
Thursday, 17 July 2025
- [AMBER] How are the A and B coefficients for LJ parameters determined? Markowska
- Re: [AMBER] How are the A and B coefficients for LJ parameters determined? Markowska
- Re: [AMBER] How are the A and B coefficients for LJ parameters determined? Markowska
- [AMBER] Negative Temperature Bug with Belly Dynamics Matthew Tremblay via AMBER
Friday, 18 July 2025
- [AMBER] Problems in installing AmberTools25 Simona Saporiti via AMBER
- Re: [AMBER] Problems in installing AmberTools25 Li, Zhen via AMBER
- Re: [AMBER] pmemd.cuda in Amber24 is failing all test (RTX 5090 + CUDA 12.9) Biplab Ghosh via AMBER
Saturday, 19 July 2025
- [AMBER] Differences in Umbrella Sampling between Amber18 and Amber24 Aadarsh Raghunathan via AMBER
Monday, 21 July 2025
- [AMBER] MMPBSA.py results unresponsive to changes in epsin Johann, Timothy via AMBER
- [AMBER] MMPBSA.py results unresponsive to changes in epsin Johann, Timothy via AMBER
- Re: [AMBER] MMPBSA.py results unresponsive to changes in epsin Ray Luo via AMBER
- Re: [AMBER] MMPBSA.py results unresponsive to changes in epsin Johann, Timothy via AMBER
- Re: [AMBER] AMBER Digest, Vol 4760, Issue 1 Kriti Shukla via AMBER
- Re: [AMBER] Differences in Umbrella Sampling between Amber18 and Amber24 Sidharth E K via AMBER
Wednesday, 23 July 2025
- [AMBER] different memory usage by Amber16 and Amber24 Umut Çağan Uçar via AMBER
Thursday, 24 July 2025
- Re: [AMBER] MMPBSA.py results unresponsive to changes in epsin David A Case via AMBER
- Re: [AMBER] different memory usage by Amber16 and Amber24 David A Case via AMBER
- [AMBER] MD simulations running slowly Lucas Gasparello Viviani via AMBER
Sunday, 27 July 2025
- [AMBER] Problems with MMPB/MMGBSA Johnny Su via AMBER
Tuesday, 29 July 2025
- [AMBER] CIF parsing needs to be updated Istvan Kolossvary via AMBER
Thursday, 31 July 2025
- Re: [AMBER] To calculate the volume of an octahedral box Daniel Roe via AMBER
- [AMBER] Help with optimizing the time of calculation Lucas Gasparello Viviani via AMBER

Last message date: Thu Jul 31 2025 - 14:30:02 PDT
Archived on: Mon Aug 11 2025 - 05:56:15 PDT