Amber Archive Aug 2025 by author

53 messages: Starting Thu Jul 31 2025 - 12:00:03 PDT, Ending Thu Aug 14 2025 - 07:00:03 PDT
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Adam Huffman via AMBER
- [AMBER] Previous versions of Amber (Fri Aug 01 2025 - 04:46:01 PDT)
Beierlein, Frank via AMBER
- [AMBER] TI Problem (Thu Aug 14 2025 - 06:34:28 PDT)
Carlos Simmerling via AMBER
- Re: [AMBER] How to define pseudodihedral angle in the DISANG file for Umbrella Sampling Simulation in AMBER? (Fri Aug 08 2025 - 05:12:18 PDT)
- Re: [AMBER] How to define pseudodihedral angle in the DISANG file for Umbrella Sampling Simulation in AMBER? (Fri Aug 08 2025 - 02:32:44 PDT)
- Re: [AMBER] CCYM missing (Sun Aug 03 2025 - 13:33:02 PDT)
Carmi, Jason R via AMBER
- Re: [AMBER] Problems with MMPB/MMGBSA (Wed Aug 06 2025 - 17:30:00 PDT)
Charo del Genio via AMBER
- Re: [AMBER] Parameterizing cisplatin with MCPB.py (Wed Aug 13 2025 - 05:27:15 PDT)
Cherry, Kendall via AMBER
- [AMBER] Error: Incompatible CUDA and GNU versions when trying to install Amber (Mon Aug 11 2025 - 14:21:06 PDT)
Christina Bergonzo via AMBER
- Re: [AMBER] Help with optimizing the time of calculation (Fri Aug 01 2025 - 05:00:13 PDT)
Daniel Roe via AMBER
- Re: [AMBER] LEaP inconsistent peripheral improper atom ordering (Tue Aug 12 2025 - 06:02:34 PDT)
David A Case via AMBER
- Re: [AMBER] Error: Incompatible CUDA and GNU versions when trying to install Amber (Tue Aug 12 2025 - 10:23:09 PDT)
- Re: [AMBER] .rst file not generated during heating step, simulation stops (Sat Aug 09 2025 - 07:01:10 PDT)
- Re: [AMBER] Numerical Instability in Umbrella Sampling (Sat Aug 02 2025 - 14:21:16 PDT)
- Re: [AMBER] Line minimizer abort while doing mmpbsa and Normal mode analysis (Sat Aug 02 2025 - 14:13:30 PDT)
- Re: [AMBER] CCYM missing (Sat Aug 02 2025 - 14:09:32 PDT)
- Re: [AMBER] Previous versions of Amber (Sat Aug 02 2025 - 13:48:12 PDT)
- Re: [AMBER] Problems with MMPB/MMGBSA (Sat Aug 02 2025 - 13:39:14 PDT)
- Re: [AMBER] MD simulations running slowly (Sat Aug 02 2025 - 13:34:29 PDT)
Dulal Mondal via AMBER
- Re: [AMBER] findgrep.py error (Sat Aug 09 2025 - 02:25:46 PDT)
- Re: [AMBER] findgrep.py error (Sat Aug 09 2025 - 01:04:22 PDT)
- Re: [AMBER] findgrep.py error (Fri Aug 08 2025 - 20:35:03 PDT)
- Re: [AMBER] findgrep.py error (Fri Aug 08 2025 - 01:55:23 PDT)
- Re: [AMBER] findgrep.py error (Fri Aug 08 2025 - 01:05:55 PDT)
- [AMBER] findgrep.py error (Wed Aug 06 2025 - 23:12:10 PDT)
Evan Pretti via AMBER
- [AMBER] LEaP inconsistent peripheral improper atom ordering (Mon Aug 11 2025 - 15:57:27 PDT)
Gourav Das via AMBER
- [AMBER] How to define pseudodihedral angle in the DISANG file for Umbrella Sampling Simulation in AMBER? (Fri Aug 08 2025 - 02:27:11 PDT)
Jeffrey Wagner via AMBER
- Re: [AMBER] MCPB.py Error at Step 2: TypeError with numpy.complex128 in angle parameter generation (Fri Aug 01 2025 - 09:18:28 PDT)
Li, Zhen via AMBER
- Re: [AMBER] Error: Incompatible CUDA and GNU versions when trying to install Amber (Tue Aug 12 2025 - 08:32:34 PDT)
- Re: [AMBER] MCPB.py Error at Step 2: TypeError with numpy.complex128 in angle parameter generation (Fri Aug 01 2025 - 11:27:34 PDT)
maciej.spiegel via AMBER
- Re: [AMBER] [Potencjalny SPAM] Re: MCPB.py Error at Step 2: TypeError with numpy.complex128 in angle parameter generation (Fri Aug 01 2025 - 12:34:26 PDT)
- [AMBER] MCPB.py Error at Step 2: TypeError with numpy.complex128 in angle parameter generation (Fri Aug 01 2025 - 08:23:49 PDT)
MAMTA YADAV via AMBER
- [AMBER] To calculate the volume of an octahedral box (Thu Jul 31 2025 - 11:30:41 PDT)
Markowska
- Re: [AMBER] Segmentation fault when running on GPU, working fine on CPU (Mon Aug 11 2025 - 02:43:48 PDT)
- Re: [AMBER] Segmentation fault when running on GPU, working fine on CPU (Fri Aug 08 2025 - 02:51:18 PDT)
- [AMBER] Segmentation fault when running on GPU, working fine on CPU (Sat Aug 02 2025 - 10:49:39 PDT)
Prithviraj Nandigrami via AMBER
- [AMBER] ASMD simulation of protein-protein complex (Fri Aug 01 2025 - 09:31:14 PDT)
Priyasha Majee via AMBER
- Re: [AMBER] Line minimizer abort while doing mmpbsa and Normal mode analysis (Fri Aug 01 2025 - 23:24:08 PDT)
- [AMBER] Line minimizer abort while doing mmpbsa and Normal mode analysis (Fri Aug 01 2025 - 10:29:57 PDT)
Scott Brozell via AMBER
- Re: [AMBER] Compilation with MVAPICH2-GDR (Tue Aug 05 2025 - 13:59:41 PDT)
Simona Saporiti via AMBER
- [AMBER] CCYM missing (Fri Aug 01 2025 - 09:38:17 PDT)
Stefan Ivanov via AMBER
- [AMBER] Parameterizing cisplatin with MCPB.py (Wed Aug 13 2025 - 05:09:31 PDT)
Sudipti Priyadarsinee via AMBER
- [AMBER] Numerical Instability in Umbrella Sampling (Sat Aug 02 2025 - 00:09:14 PDT)
Timothy Giese via AMBER
- Re: [AMBER] Problem of water breaking in coordinate file. (Thu Aug 07 2025 - 08:58:20 PDT)
- Re: [AMBER] Problem of water breaking in coordinate file. (Wed Aug 06 2025 - 07:00:28 PDT)
Vinicius Cruzeiro via AMBER
- Re: [AMBER] findgrep.py error (Sat Aug 09 2025 - 12:05:56 PDT)
- Re: [AMBER] findgrep.py error (Sat Aug 09 2025 - 01:18:25 PDT)
- Re: [AMBER] findgrep.py error (Fri Aug 08 2025 - 20:54:12 PDT)
- Re: [AMBER] findgrep.py error (Fri Aug 08 2025 - 19:19:54 PDT)
YASHIKA . via AMBER
- [AMBER] segmentation fault error (Thu Aug 14 2025 - 06:52:39 PDT)
- [AMBER] .rst file not generated during heating step, simulation stops (Fri Aug 08 2025 - 23:03:45 PDT)
- Re: [AMBER] Problem of water breaking in coordinate file. (Wed Aug 06 2025 - 03:46:02 PDT)
Yasser Almeida via AMBER
- [AMBER] Compilation with MVAPICH2-GDR (Mon Aug 04 2025 - 02:05:49 PDT)
Zihao Bai via AMBER
- [AMBER] Bug in PMEMD Plumed Compilation in Amber24 (Wed Aug 13 2025 - 10:57:35 PDT)