Amber Archive Jun 2023 by messages with attachments

152 messages: Starting Thu Jun 01 2023 - 00:00:03 PDT, Ending Fri Jun 30 2023 - 13:30:02 PDT
This period: Most recent messages
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[AMBER] umbrella sampling angad sharma via AMBER (Sun Jun 04 2023 - 14:03:37 PDT)
1. histoi1.png (304510 bytes)
2. pmf.png (6070 bytes)
[AMBER] RNA with 5' phosphates Michael Bruist via AMBER (Mon Jun 05 2023 - 11:07:17 PDT)
1. tleap_commands.txt (321 bytes)
2. TLS1_clipped_K.inmin (116 bytes)
3. GMP_failure.mp4 (236069 bytes)
Re: [AMBER] Self Inconsistency within antechamber for NAD and NAP cofactors (expects different bond orders in different routines) Christopher Corbo via AMBER (Mon Jun 05 2023 - 20:23:38 PDT)
1. 2F38.cof.am1bcc.mol2 (8015 bytes)
2. 3LSY.cof.processed.mol2 (7614 bytes)
3. 3LSY.cof.am1bcc.mol2 (7697 bytes)
4. 2F38.cof.processed.mol2 (7917 bytes)
[AMBER] Tolerance problem in umbrella sampling angad sharma via AMBER (Tue Jun 06 2023 - 02:29:00 PDT)
1. tolerance.png (39621 bytes)
[AMBER] huge memory consumption when running nab simulations Dominik Brandstetter via AMBER (Tue Jun 06 2023 - 05:32:47 PDT)
1. sim.nab (760 bytes)
2. submit.sh (531 bytes)
[AMBER] Serial Installation: 26 errors detected in the compilation of "/software/Amber22AmberTools23/amber22_src/src/pmemd/src/xray/cuda/src/xray/BulkMaskGPU.cu". Pertschy, Florian via AMBER (Tue Jun 06 2023 - 05:39:20 PDT)
1. buildlog.txt (49698 bytes)
[AMBER] Radii doubt during MCPB.py parametrization Mario Lopez Martin via AMBER (Fri Jun 23 2023 - 01:42:58 PDT)
1. ms3tjbsn.png (12243 bytes)
2. qnjrdn5t.png (982 bytes)
3. nnffgvsn.png (604 bytes)
4. vg2mnc3c.png (833 bytes)
[AMBER] Issue about atomic forces acting on each atom 簡羲煥 via AMBER (Fri Jun 23 2023 - 03:35:42 PDT)
1. 1687514909956.png (53542 bytes)
2. 1687515048052.png (26581 bytes)
3. 1687515158954.png (347536 bytes)
[AMBER] Energy bumps and structure deformation while minimization of a small molecule Kotaro TANAKA via AMBER (Tue Jun 27 2023 - 22:16:41 PDT)
1. 230628_energy.png (18438 bytes)
2. min.out (392616 bytes)
3. frame478.png (64155 bytes)
4. frame479.png (66124 bytes)
5. frame480.png (65649 bytes)
6. frame481.png (64090 bytes)