Amber Archive Jun 2023: by subject

[AMBER] [Sender Not Verified] About polar solvation term in MMGBSA decomposition results
- Steinbrecher, Thomas via AMBER (Tue Jun 13 2023 - 23:47:05 PDT)
[AMBER] [Sender Not Verified] Atom musk selection error
- Tanmoy Paul via AMBER (Mon Jun 05 2023 - 00:41:07 PDT)
[AMBER] [Sender Not Verified] Determine whether water molecules are with 1 Å of crystal waters from the PDB structure during the MD simulation
- Eduard Neu via AMBER (Tue Jun 27 2023 - 10:07:46 PDT)
- Steinbrecher, Thomas via AMBER (Wed Jun 21 2023 - 23:42:03 PDT)
[AMBER] [Sender Not Verified] Problems with minimization energy NaN
- Steinbrecher, Thomas via AMBER (Fri Jun 02 2023 - 07:34:09 PDT)
[AMBER] [Sender Not Verified] Regarding Determination of HIS Residue States
- zhangxiaochun via AMBER (Mon Jun 12 2023 - 03:14:40 PDT)
- Steinbrecher, Thomas via AMBER (Mon Jun 12 2023 - 02:51:42 PDT)
[AMBER] [Sender Not Verified] RNA with 5' phosphates
- Steinbrecher, Thomas via AMBER (Mon Jun 05 2023 - 23:23:21 PDT)
[AMBER] [Sender Not Verified] Running gas phase TI with pmemd.CUDA.
- Steinbrecher, Thomas via AMBER (Mon Jun 05 2023 - 02:23:27 PDT)
- Fanyu Zhao via AMBER (Mon Jun 05 2023 - 01:34:58 PDT)
- Steinbrecher, Thomas via AMBER (Mon Jun 05 2023 - 01:02:03 PDT)
- Fanyu Zhao via AMBER (Mon Jun 05 2023 - 00:41:55 PDT)
[AMBER] A script to build Amber on a Cray EX supercomputer with AMD GPU support
- Cristian Di Pietrantonio via AMBER (Wed Jun 28 2023 - 05:46:08 PDT)
- David A Case via AMBER (Wed Jun 28 2023 - 05:18:24 PDT)
- Cristian Di Pietrantonio via AMBER (Wed Jun 28 2023 - 02:05:56 PDT)
[AMBER] About polar solvation term in MMGBSA decomposition results
- xiangyu via AMBER (Tue Jun 13 2023 - 18:57:56 PDT)
[AMBER] amber 22 installation
- David A Case via AMBER (Sun Jun 18 2023 - 05:01:04 PDT)
- Dulal Mondal via AMBER (Sat Jun 17 2023 - 06:30:28 PDT)
[AMBER] AMBER calculation limitatation
- David A Case via AMBER (Tue Jun 20 2023 - 15:15:58 PDT)
- 刘野 via AMBER (Thu Jun 08 2023 - 18:45:28 PDT)
[AMBER] Amber22/Tools23 M2 Mac installation
- Xavier Brazzolotto via AMBER (Tue Jun 20 2023 - 07:19:10 PDT)
- Xavier Brazzolotto via AMBER (Tue Jun 20 2023 - 02:13:18 PDT)
[AMBER] AMD GPU install problems
- Charo del Genio via AMBER (Tue Jun 06 2023 - 02:56:24 PDT)
- Derek M Shore via AMBER (Mon Jun 05 2023 - 09:22:21 PDT)
[AMBER] AMD GPU install problems (David A Case)
- Charo del Genio via AMBER (Fri Jun 09 2023 - 05:51:13 PDT)
- Derek M Shore via AMBER (Thu Jun 08 2023 - 11:39:05 PDT)
[AMBER] an-initio folding simulation
- Prithviraj Nandigrami via AMBER (Mon Jun 05 2023 - 14:16:48 PDT)
[AMBER] Atom musk selection error
- Tanmoy Paul via AMBER (Sat Jun 03 2023 - 22:51:21 PDT)
[AMBER] Atom selection in cpptraj
- SATYAJIT KHATUA via AMBER (Sat Jun 10 2023 - 07:43:48 PDT)
- Daniel Roe via AMBER (Sat Jun 10 2023 - 07:38:27 PDT)
- Erik Zuiderweg via AMBER (Sat Jun 10 2023 - 07:33:57 PDT)
[AMBER] Can L4 GPU cards be used with AMBER 22?
- Ross Walker via AMBER (Thu Jun 22 2023 - 08:51:17 PDT)
- Ilyas Yildirim via AMBER (Thu Jun 22 2023 - 08:33:36 PDT)
- Ross Walker via AMBER (Thu Jun 22 2023 - 08:26:45 PDT)
[AMBER] closest command cpptraj
- Daniel Roe via AMBER (Thu Jun 01 2023 - 10:31:11 PDT)
- Maria Bzówka via AMBER (Wed May 31 2023 - 23:38:04 PDT)
[AMBER] Cluster size
- Daniel Roe via AMBER (Fri Jun 09 2023 - 08:08:39 PDT)
[AMBER] Compiling Amber 22 (+ AT 23) with Intel compiler
- Vlad Cojocaru via AMBER (Mon Jun 05 2023 - 06:58:06 PDT)
- David A Case via AMBER (Mon Jun 05 2023 - 04:58:24 PDT)
- Vlad Cojocaru via AMBER (Sun Jun 04 2023 - 23:23:34 PDT)
[AMBER] Compiling amber/Tools22 in Ubuntu 22.04
- David A Case via AMBER (Thu Jun 22 2023 - 14:34:23 PDT)
- Pablo Galaz-Davison via AMBER (Thu Jun 22 2023 - 13:27:11 PDT)
[AMBER] Constant pH remd in amber
- Jason Swails via AMBER (Wed Jun 28 2023 - 05:11:09 PDT)
- Dulal Mondal via AMBER (Thu Jun 22 2023 - 07:21:34 PDT)
[AMBER] Contant pH REMD run in amber22 using pmemd.cuda.MPI
- Dulal Mondal via AMBER (Mon Jun 26 2023 - 21:52:48 PDT)
[AMBER] Correct interpretation of mmgbsa decomposition results
- 鱼翔 via AMBER (Sun Jun 11 2023 - 11:03:48 PDT)
[AMBER] cpptraj and nastruct
- Daniel Roe via AMBER (Fri Jun 30 2023 - 11:28:12 PDT)
- Daniel Roe via AMBER (Thu Jun 29 2023 - 05:58:32 PDT)
- Daniel Roe via AMBER (Mon Jun 26 2023 - 05:51:40 PDT)
- Jing Qu via AMBER (Sun Jun 25 2023 - 21:35:37 PDT)
[AMBER] Determine whether water molecules are with 1 Å of crystal waters from the PDB structure during the MD simulation
- Daniel Roe via AMBER (Thu Jun 29 2023 - 06:10:49 PDT)
- Daniel Roe via AMBER (Thu Jun 22 2023 - 07:00:35 PDT)
- Eduard Neu via AMBER (Wed Jun 21 2023 - 14:25:47 PDT)
[AMBER] Diffusion in pmemd.cuda
- Daniel Roe via AMBER (Fri Jun 09 2023 - 06:47:18 PDT)
- David A Case via AMBER (Fri Jun 09 2023 - 05:28:54 PDT)
- David Poole via AMBER (Thu Jun 08 2023 - 11:20:51 PDT)
[AMBER] electric field availability in the CUDA code
- Sally Pias via AMBER (Tue Jun 20 2023 - 08:50:03 PDT)
- Sally Pias via AMBER (Thu Jun 15 2023 - 05:00:00 PDT)
[AMBER] Electrostatic potential calculation of the active site
- Dulal Mondal via AMBER (Mon Jun 26 2023 - 03:27:27 PDT)
[AMBER] Energy bumps and structure deformation while minimization of a small molecule
- Kotaro TANAKA via AMBER (Wed Jun 28 2023 - 06:04:03 PDT)
- David A Case via AMBER (Wed Jun 28 2023 - 05:20:40 PDT)
- Kotaro TANAKA via AMBER (Tue Jun 27 2023 - 22:16:41 PDT)
[AMBER] error in amber installation with cuda 9.0
- David A Case via AMBER (Thu Jun 22 2023 - 09:02:47 PDT)
- 홍종희 via AMBER (Tue Jun 20 2023 - 01:53:43 PDT)
[AMBER] error in amber22 installation
- 홍종희 via AMBER (Thu Jun 08 2023 - 21:43:17 PDT)
- David A Case via AMBER (Thu Jun 08 2023 - 06:11:51 PDT)
- 홍종희 via AMBER (Wed Jun 07 2023 - 23:43:20 PDT)
[AMBER] Error in modelling with ion using MCPB.py
- Abhilash J via AMBER (Mon Jun 26 2023 - 16:49:26 PDT)
- Abhilash J via AMBER (Mon Jun 19 2023 - 20:53:04 PDT)
[AMBER] Error in running mmpbsa and mmgbsa
- AMANPREET KAUR via AMBER (Sun Jun 18 2023 - 23:59:31 PDT)
[AMBER] Error while running mmpbsa
- SATYAJIT KHATUA via AMBER (Mon Jun 19 2023 - 01:55:23 PDT)
- SATYAJIT KHATUA via AMBER (Mon Jun 19 2023 - 00:44:27 PDT)
- SATYAJIT KHATUA via AMBER (Mon Jun 19 2023 - 00:37:43 PDT)
- SATYAJIT KHATUA via AMBER (Sun Jun 18 2023 - 23:29:00 PDT)
- SATYAJIT KHATUA via AMBER (Sun Jun 18 2023 - 22:14:34 PDT)
- AMANPREET KAUR via AMBER (Sun Jun 18 2023 - 22:01:16 PDT)
- Prithviraj Nandigrami via AMBER (Sat Jun 17 2023 - 03:11:35 PDT)
- AMANPREET KAUR via AMBER (Sat Jun 17 2023 - 03:07:18 PDT)
[AMBER] ff19SB on Gromacs
- Franz Waibl via AMBER (Thu Jun 22 2023 - 00:34:26 PDT)
- Carlos Simmerling via AMBER (Wed Jun 21 2023 - 09:07:59 PDT)
- Franz Waibl via AMBER (Wed Jun 21 2023 - 08:25:32 PDT)
- Carlos Simmerling via AMBER (Wed Jun 21 2023 - 07:52:53 PDT)
- Franz Waibl via AMBER (Wed Jun 21 2023 - 07:28:42 PDT)
- Carlos Simmerling via AMBER (Wed Jun 21 2023 - 06:14:01 PDT)
- Franz Waibl via AMBER (Wed Jun 21 2023 - 05:58:51 PDT)
[AMBER] Fwd: [Sender Not Verified] Electrostatic potential calculation of the active site
- Ray Luo via AMBER (Mon Jun 26 2023 - 08:16:15 PDT)
- Dulal Mondal via AMBER (Mon Jun 26 2023 - 04:03:24 PDT)
[AMBER] group pdb in clusters
- King Wu via AMBER (Wed Jun 14 2023 - 21:48:56 PDT)
[AMBER] H-bond analysis in cpptraj
- Prithviraj Nandigrami via AMBER (Wed Jun 07 2023 - 11:46:53 PDT)
[AMBER] huge memory consumption when running nab simulations
- Dominik Brandstetter via AMBER (Fri Jun 16 2023 - 06:15:12 PDT)
- Dominik Brandstetter via AMBER (Tue Jun 13 2023 - 06:10:26 PDT)
- David A Case via AMBER (Mon Jun 12 2023 - 17:57:16 PDT)
- Dominik Brandstetter via AMBER (Sun Jun 11 2023 - 23:46:16 PDT)
- Charo del Genio via AMBER (Tue Jun 06 2023 - 09:42:02 PDT)
- Dominik Brandstetter via AMBER (Tue Jun 06 2023 - 05:32:47 PDT)
[AMBER] Issue about atomic forces acting on each atom
- 簡羲煥 via AMBER (Tue Jun 27 2023 - 04:36:02 PDT)
- Daniel Roe via AMBER (Mon Jun 26 2023 - 05:49:07 PDT)
- David A Case via AMBER (Sat Jun 24 2023 - 04:55:34 PDT)
- 簡羲煥 via AMBER (Fri Jun 23 2023 - 03:35:42 PDT)
[AMBER] kerror about mmpbsa
- SATYAJIT KHATUA via AMBER (Thu Jun 29 2023 - 23:34:35 PDT)
- ZangRiran via AMBER (Thu Jun 29 2023 - 18:55:37 PDT)
[AMBER] Keyerror about mmpbsa
- SATYAJIT KHATUA via AMBER (Wed Jun 28 2023 - 01:43:46 PDT)
- ZangRiran via AMBER (Tue Jun 27 2023 - 00:20:17 PDT)
- SATYAJIT KHATUA via AMBER (Mon Jun 26 2023 - 08:48:29 PDT)
- Ray Luo via AMBER (Mon Jun 26 2023 - 08:00:59 PDT)
- 余鸿艳 via AMBER (Sun Jun 25 2023 - 22:16:59 PDT)
[AMBER] MCPB.py returns "ZeroDivisionError: float division by zero" in step 2
- Maciej Spiegel via AMBER (Sun Jun 04 2023 - 03:43:06 PDT)
[AMBER] Mix solvent MD
- King Wu via AMBER (Fri Jun 30 2023 - 13:14:44 PDT)
[AMBER] Modified nucleic acid parameters
- Jenny 148 via AMBER (Thu Jun 22 2023 - 23:38:54 PDT)
[AMBER] Native contacts analysis in CPPTRAJ
- Prithviraj Nandigrami via AMBER (Wed Jun 07 2023 - 11:56:41 PDT)
[AMBER] OPC vs. TIP3P
- Giulia Palermo via AMBER (Sat Jun 17 2023 - 19:02:26 PDT)
[AMBER] Probability of Contact Formation
- Aravind R via AMBER (Mon Jun 12 2023 - 09:20:57 PDT)
[AMBER] Problems with minimization energy NaN
- Bhattacharjee, Sinjini via AMBER (Wed Jun 07 2023 - 05:49:51 PDT)
- David A Case via AMBER (Wed Jun 07 2023 - 05:27:59 PDT)
- David A Case via AMBER (Fri Jun 02 2023 - 09:03:29 PDT)
- Prithviraj Nandigrami via AMBER (Fri Jun 02 2023 - 07:33:31 PDT)
- Carlos Simmerling via AMBER (Fri Jun 02 2023 - 07:32:12 PDT)
- Bhattacharjee, Sinjini via AMBER (Fri Jun 02 2023 - 07:26:43 PDT)
[AMBER] qm/mmpbsa calculations
- Bill Miller III via AMBER (Fri Jun 23 2023 - 08:54:14 PDT)
- Hector A. Baldoni via AMBER (Thu Jun 22 2023 - 16:06:26 PDT)
[AMBER] Radii doubt during MCPB.py parametrization
- Mario Lopez Martin via AMBER (Fri Jun 23 2023 - 01:42:58 PDT)
[AMBER] Regarding Determination of HIS Residue States
- zhangxiaochun via AMBER (Mon Jun 12 2023 - 01:14:51 PDT)
[AMBER] Regarding K-means clustering
- Daniel Roe via AMBER (Wed Jun 14 2023 - 11:34:46 PDT)
- Saikat Pal via AMBER (Wed Jun 14 2023 - 11:05:37 PDT)
[AMBER] RNA with 5' phosphates
- Michael Bruist via AMBER (Mon Jun 05 2023 - 11:07:17 PDT)
[AMBER] Rotational PMF Question
- Matthew Guberman-Pfeffer via AMBER (Fri Jun 09 2023 - 23:58:18 PDT)
[AMBER] Running gas phase TI with pmemd.CUDA.
- Fanyu Zhao via AMBER (Sun Jun 04 2023 - 19:25:29 PDT)
[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)
- David A Case via AMBER (Mon Jun 05 2023 - 13:50:59 PDT)
- Christopher Corbo via AMBER (Mon Jun 05 2023 - 13:36:17 PDT)
[AMBER] Serial Installation: 26 errors detected in the compilation of "/software/Amber22AmberTools23/amber22_src/src/pmemd/src/xray/cuda/src/xray/BulkMaskGPU.cu".
- David A Case via AMBER (Tue Jun 06 2023 - 09:26:09 PDT)
- Pertschy, Florian via AMBER (Tue Jun 06 2023 - 05:39:20 PDT)
[AMBER] Simulation protocol for Ionic Liquid (IL) - Bilayer system
- Delwakkada Liyanage, Senal Dinuka via AMBER (Sun Jun 04 2023 - 12:01:03 PDT)
[AMBER] Tolerance problem in umbrella sampling
- angad sharma via AMBER (Tue Jun 06 2023 - 02:29:00 PDT)
[AMBER] Trouble Installing OpenMPI on Amazon Linux 2 (Centos)
- David A Case via AMBER (Wed Jun 07 2023 - 18:25:58 PDT)
- Evan Biedermann via AMBER (Wed Jun 07 2023 - 10:12:40 PDT)
[AMBER] umbrella sampling
- angad sharma via AMBER (Sun Jun 04 2023 - 14:03:37 PDT)
[AMBER] unsuscribe
- Ryan Novosielski via AMBER (Wed Jun 28 2023 - 11:23:17 PDT)
- Monsurat M. Lawal via AMBER (Wed Jun 28 2023 - 09:53:13 PDT)
- Daniel Konstantinovsky via AMBER (Wed Jun 28 2023 - 08:07:36 PDT)
[AMBER] Using plumed with amber
- David A Case via AMBER (Wed Jun 28 2023 - 05:22:57 PDT)
- Songyan Xia \(LHS, 118010341\) via AMBER (Tue Jun 27 2023 - 19:37:15 PDT)
[AMBER] 回复: cpptraj and nastruct
- Huang ZiJian via AMBER (Tue Jun 27 2023 - 19:28:03 PDT)
[AMBER] 回复: Issue about atomic forces acting on each atom
- 簡羲煥 via AMBER (Tue Jun 27 2023 - 04:36:12 PDT)
- Huang ZiJian via AMBER (Fri Jun 23 2023 - 20:46:04 PDT)
[AMBER] 回复: Keyerror about mmpbsa
- ZangRiran via AMBER (Thu Jun 29 2023 - 00:55:46 PDT)
- Huang ZiJian via AMBER (Tue Jun 27 2023 - 20:17:12 PDT)
[AMBER] 回复: Using plumed with amber
- Songyan Xia \(LHS, 118010341\) via AMBER (Wed Jun 28 2023 - 19:21:44 PDT)
[AMBER] 回复: 回复: Issue about atomic forces acting on each atom
- Daniel Roe via AMBER (Thu Jun 29 2023 - 06:04:22 PDT)
- Huang ZiJian via AMBER (Tue Jun 27 2023 - 19:13:29 PDT)
[Sender Not Verified] Determine whether water molecules are with 1 Å of crystal waters from the PDB structure during the MD simulation
- Steinbrecher, Thomas via AMBER (Tue Jun 27 2023 - 23:07:41 PDT)
Issues with simulating 5'-phosphorylated RNA strands
- Michael Bruist via AMBER (Mon Jun 19 2023 - 09:53:04 PDT)

Amber Archive Jun 2023 by subject