Amber Archive Jun 2023: by date

Wednesday, 31 May 2023
- [AMBER] closest command cpptraj Maria Bzówka via AMBER
Thursday, 1 June 2023
- Re: [AMBER] closest command cpptraj Daniel Roe via AMBER
Friday, 2 June 2023
- [AMBER] Problems with minimization energy NaN Bhattacharjee, Sinjini via AMBER
- Re: [AMBER] Problems with minimization energy NaN Carlos Simmerling via AMBER
- Re: [AMBER] Problems with minimization energy NaN Prithviraj Nandigrami via AMBER
- Re: [AMBER] [Sender Not Verified] Problems with minimization energy NaN Steinbrecher, Thomas via AMBER
- Re: [AMBER] Problems with minimization energy NaN David A Case via AMBER
Saturday, 3 June 2023
- [AMBER] Atom musk selection error Tanmoy Paul via AMBER
Sunday, 4 June 2023
- [AMBER] MCPB.py returns "ZeroDivisionError: float division by zero" in step 2 Maciej Spiegel via AMBER
- [AMBER] Simulation protocol for Ionic Liquid (IL) - Bilayer system Delwakkada Liyanage, Senal Dinuka via AMBER
- [AMBER] umbrella sampling angad sharma via AMBER
- [AMBER] Running gas phase TI with pmemd.CUDA. Fanyu Zhao via AMBER
- [AMBER] Compiling Amber 22 (+ AT 23) with Intel compiler Vlad Cojocaru via AMBER
Monday, 5 June 2023
- Re: [AMBER] [Sender Not Verified] Atom musk selection error Tanmoy Paul via AMBER
- Re: [AMBER] [Sender Not Verified] Running gas phase TI with pmemd.CUDA. Fanyu Zhao via AMBER
- Re: [AMBER] [Sender Not Verified] Running gas phase TI with pmemd.CUDA. Steinbrecher, Thomas via AMBER
- Re: [AMBER] [Sender Not Verified] Running gas phase TI with pmemd.CUDA. Fanyu Zhao via AMBER
- Re: [AMBER] [Sender Not Verified] Running gas phase TI with pmemd.CUDA. Steinbrecher, Thomas via AMBER
- Re: [AMBER] Compiling Amber 22 (+ AT 23) with Intel compiler David A Case via AMBER
- Re: [AMBER] Compiling Amber 22 (+ AT 23) with Intel compiler Vlad Cojocaru via AMBER
- [AMBER] AMD GPU install problems Derek M Shore via AMBER
- [AMBER] RNA with 5' phosphates Michael Bruist via AMBER
- [AMBER] Self Inconsistency within antechamber for NAD and NAP cofactors (expects different bond orders in different routines) Christopher Corbo via AMBER
- Re: [AMBER] Self Inconsistency within antechamber for NAD and NAP cofactors (expects different bond orders in different routines) David A Case via AMBER
- [AMBER] an-initio folding simulation Prithviraj Nandigrami via AMBER
- Re: [AMBER] Self Inconsistency within antechamber for NAD and NAP cofactors (expects different bond orders in different routines) Christopher Corbo via AMBER
- Re: [AMBER] [Sender Not Verified] RNA with 5' phosphates Steinbrecher, Thomas via AMBER
Tuesday, 6 June 2023
- [AMBER] Tolerance problem in umbrella sampling angad sharma via AMBER
- Re: [AMBER] AMD GPU install problems Charo del Genio via AMBER
- [AMBER] huge memory consumption when running nab simulations Dominik Brandstetter via AMBER
- [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
- Re: [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
- Re: [AMBER] huge memory consumption when running nab simulations Charo del Genio via AMBER
Wednesday, 7 June 2023
- Re: [AMBER] Problems with minimization energy NaN David A Case via AMBER
- Re: [AMBER] Problems with minimization energy NaN Bhattacharjee, Sinjini via AMBER
- [AMBER] Trouble Installing OpenMPI on Amazon Linux 2 (CentOS) Evan Biedermann via AMBER
- [AMBER] H-bond analysis in cpptraj Prithviraj Nandigrami via AMBER
- [AMBER] Native contacts analysis in CPPTRAJ Prithviraj Nandigrami via AMBER
- Re: [AMBER] Trouble Installing OpenMPI on Amazon Linux 2 (Centos) David A Case via AMBER
- [AMBER] error in amber22 installation 홍종희 via AMBER
Thursday, 8 June 2023
- Re: [AMBER] error in amber22 installation David A Case via AMBER
- [AMBER] Diffusion in pmemd.cuda David Poole via AMBER
- Re: [AMBER] AMD GPU install problems (David A Case) Derek M Shore via AMBER
- [AMBER] AMBER calculation limitatation 刘野 via AMBER
- Re: [AMBER] error in amber22 installation 홍종희 via AMBER
Friday, 9 June 2023
- Re: [AMBER] Diffusion in pmemd.cuda David A Case via AMBER
- Re: [AMBER] AMD GPU install problems (David A Case) Charo del Genio via AMBER
- Re: [AMBER] Diffusion in pmemd.cuda Daniel Roe via AMBER
- Re: [AMBER] Cluster size Daniel Roe via AMBER
- [AMBER] Rotational PMF Question Matthew Guberman-Pfeffer via AMBER
Saturday, 10 June 2023
- [AMBER] Atom selection in cpptraj Erik Zuiderweg via AMBER
- Re: [AMBER] Atom selection in cpptraj Daniel Roe via AMBER
- Re: [AMBER] Atom selection in cpptraj SATYAJIT KHATUA via AMBER
Sunday, 11 June 2023
- [AMBER] Correct interpretation of mmgbsa decomposition results 鱼翔 via AMBER
- Re: [AMBER] huge memory consumption when running nab simulations Dominik Brandstetter via AMBER
Monday, 12 June 2023
- [AMBER] Regarding Determination of HIS Residue States zhangxiaochun via AMBER
- Re: [AMBER] [Sender Not Verified] Regarding Determination of HIS Residue States Steinbrecher, Thomas via AMBER
- Re: [AMBER] [Sender Not Verified] Regarding Determination of HIS Residue States zhangxiaochun via AMBER
- [AMBER] Probability of Contact Formation Aravind R via AMBER
- Re: [AMBER] huge memory consumption when running nab simulations David A Case via AMBER
Tuesday, 13 June 2023
- Re: [AMBER] huge memory consumption when running nab simulations Dominik Brandstetter via AMBER
- [AMBER] About polar solvation term in MMGBSA decomposition results xiangyu via AMBER
- Re: [AMBER] [Sender Not Verified] About polar solvation term in MMGBSA decomposition results Steinbrecher, Thomas via AMBER
Wednesday, 14 June 2023
- [AMBER] Regarding K-means clustering Saikat Pal via AMBER
- Re: [AMBER] Regarding K-means clustering Daniel Roe via AMBER
- [AMBER] group pdb in clusters King Wu via AMBER
Thursday, 15 June 2023
- [AMBER] electric field availability in the CUDA code Sally Pias via AMBER
Friday, 16 June 2023
- Re: [AMBER] huge memory consumption when running nab simulations Dominik Brandstetter via AMBER
Saturday, 17 June 2023
- [AMBER] error while running mmpbsa AMANPREET KAUR via AMBER
- Re: [AMBER] error while running mmpbsa Prithviraj Nandigrami via AMBER
- [AMBER] amber 22 installation Dulal Mondal via AMBER
- [AMBER] OPC vs. TIP3P Giulia Palermo via AMBER
Sunday, 18 June 2023
- Re: [AMBER] amber 22 installation David A Case via AMBER
- [AMBER] Error while running mmpbsa AMANPREET KAUR via AMBER
- Re: [AMBER] Error while running mmpbsa SATYAJIT KHATUA via AMBER
- Re: [AMBER] Error while running mmpbsa SATYAJIT KHATUA via AMBER
- [AMBER] Error in running mmpbsa and mmgbsa AMANPREET KAUR via AMBER
Monday, 19 June 2023
- Re: [AMBER] Error while running mmpbsa SATYAJIT KHATUA via AMBER
- Re: [AMBER] Error while running mmpbsa SATYAJIT KHATUA via AMBER
- Re: [AMBER] Error while running mmpbsa SATYAJIT KHATUA via AMBER
- Re: [AMBER] [Sender Not Verified] Re: Issues with simulating 5'-phosphorylated RNA strands Michael Bruist via AMBER
- [AMBER] Error in modelling with ion using MCPB.py Abhilash J via AMBER
Tuesday, 20 June 2023
- [AMBER] error in amber installation with cuda 9.0 홍종희 via AMBER
- [AMBER] Amber22/Tools23 M2 Mac installation Xavier Brazzolotto via AMBER
- Re: [AMBER] Amber22/Tools23 M2 Mac installation Xavier Brazzolotto via AMBER
- Re: [AMBER] electric field availability in the CUDA code Sally Pias via AMBER
- Re: [AMBER] AMBER calculation limitatation David A Case via AMBER
Wednesday, 21 June 2023
- [AMBER] ff19SB on Gromacs Franz Waibl via AMBER
- Re: [AMBER] ff19SB on Gromacs Carlos Simmerling via AMBER
- Re: [AMBER] ff19SB on Gromacs Franz Waibl via AMBER
- Re: [AMBER] ff19SB on Gromacs Carlos Simmerling via AMBER
- Re: [AMBER] ff19SB on Gromacs Franz Waibl via AMBER
- Re: [AMBER] ff19SB on Gromacs Carlos Simmerling via AMBER
- [AMBER] Determine whether water molecules are with 1 Å of crystal waters from the PDB structure during the MD simulation Eduard Neu via AMBER
- Re: [AMBER] [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
Thursday, 22 June 2023
- Re: [AMBER] ff19SB on Gromacs Franz Waibl via AMBER
- Re: [AMBER] Determine whether water molecules are with 1 Å of crystal waters from the PDB structure during the MD simulation Daniel Roe via AMBER
- [AMBER] Constant pH remd in amber Dulal Mondal via AMBER
- Re: [AMBER] Can L4 GPU cards be used with AMBER 22? Ross Walker via AMBER
- Re: [AMBER] Can L4 GPU cards be used with AMBER 22? Ilyas Yildirim via AMBER
- Re: [AMBER] Can L4 GPU cards be used with AMBER 22? Ross Walker via AMBER
- Re: [AMBER] error in amber installation with cuda 9.0 David A Case via AMBER
- [AMBER] Compiling amber/Tools22 in Ubuntu 22.04 Pablo Galaz-Davison via AMBER
- Re: [AMBER] Compiling amber/Tools22 in Ubuntu 22.04 David A Case via AMBER
- [AMBER] qm/mmpbsa calculations Hector A. Baldoni via AMBER
- [AMBER] Modified nucleic acid parameters Jenny 148 via AMBER
Friday, 23 June 2023
- [AMBER] Radii doubt during MCPB.py parametrization Mario Lopez Martin via AMBER
- [AMBER] Issue about atomic forces acting on each atom 簡羲煥 via AMBER
- Re: [AMBER] qm/mmpbsa calculations Bill Miller III via AMBER
- [AMBER] 回复: Issue about atomic forces acting on each atom Huang ZiJian via AMBER
Saturday, 24 June 2023
- Re: [AMBER] Issue about atomic forces acting on each atom David A Case via AMBER
Sunday, 25 June 2023
- [AMBER] cpptraj and nastruct Jing Qu via AMBER
- [AMBER] Keyerror about mmpbsa 余鸿艳 via AMBER
Monday, 26 June 2023
- [AMBER] Electrostatic potential calculation of the active site Dulal Mondal via AMBER
- [AMBER] Fwd: [Sender Not Verified] Electrostatic potential calculation of the active site Dulal Mondal via AMBER
- Re: [AMBER] Issue about atomic forces acting on each atom Daniel Roe via AMBER
- Re: [AMBER] cpptraj and nastruct Daniel Roe via AMBER
- Re: [AMBER] Keyerror about mmpbsa Ray Luo via AMBER
- Re: [AMBER] Fwd: [Sender Not Verified] Electrostatic potential calculation of the active site Ray Luo via AMBER
- Re: [AMBER] Keyerror about mmpbsa SATYAJIT KHATUA via AMBER
- Re: [AMBER] Error in modelling with ion using MCPB.py Abhilash J via AMBER
- [AMBER] Contant pH REMD run in amber22 using pmemd.cuda.MPI Dulal Mondal via AMBER
Tuesday, 27 June 2023
- [AMBER] Keyerror about mmpbsa ZangRiran via AMBER
- Re: [AMBER] 回复: Issue about atomic forces acting on each atom 簡羲煥 via AMBER
- Re: [AMBER] Issue about atomic forces acting on each atom 簡羲煥 via AMBER
- Re: [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
- [AMBER] 回复: 回复: Issue about atomic forces acting on each atom Huang ZiJian via AMBER
- [AMBER] 回复: cpptraj and nastruct Huang ZiJian via AMBER
- [AMBER] Using plumed with amber Songyan Xia \(LHS, 118010341\) via AMBER
- [AMBER] 回复: Keyerror about mmpbsa Huang ZiJian via AMBER
- [AMBER] Energy bumps and structure deformation while minimization of a small molecule Kotaro TANAKA via AMBER
- Re: [AMBER] [Sender Not Verified] Re: [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
Wednesday, 28 June 2023
- Re: [AMBER] Keyerror about mmpbsa SATYAJIT KHATUA via AMBER
- [AMBER] A script to build Amber on a Cray EX supercomputer with AMD GPU support Cristian Di Pietrantonio via AMBER
- Re: [AMBER] Constant pH remd in amber Jason Swails via AMBER
- Re: [AMBER] A script to build Amber on a Cray EX supercomputer with AMD GPU support David A Case via AMBER
- Re: [AMBER] Energy bumps and structure deformation while minimization of a small molecule David A Case via AMBER
- Re: [AMBER] Using plumed with amber David A Case via AMBER
- Re: [AMBER] A script to build Amber on a Cray EX supercomputer with AMD GPU support Cristian Di Pietrantonio via AMBER
- Re: [AMBER] Energy bumps and structure deformation while minimization of a small molecule Kotaro TANAKA via AMBER
- Re: [AMBER] unsuscribe Daniel Konstantinovsky via AMBER
- Re: [AMBER] unsuscribe Monsurat M. Lawal via AMBER
- Re: [AMBER] unsuscribe Ryan Novosielski via AMBER
- [AMBER] 回复: Using plumed with amber Songyan Xia \(LHS, 118010341\) via AMBER
Thursday, 29 June 2023
- Re: [AMBER] 回复: Keyerror about mmpbsa ZangRiran via AMBER
- Re: [AMBER] cpptraj and nastruct Daniel Roe via AMBER
- Re: [AMBER] 回复: 回复: Issue about atomic forces acting on each atom Daniel Roe via AMBER
- Re: [AMBER] Determine whether water molecules are with 1 Å of crystal waters from the PDB structure during the MD simulation Daniel Roe via AMBER
- [AMBER] kerror about mmpbsa ZangRiran via AMBER
- Re: [AMBER] kerror about mmpbsa SATYAJIT KHATUA via AMBER
Friday, 30 June 2023
- Re: [AMBER] cpptraj and nastruct Daniel Roe via AMBER
- [AMBER] Mix solvent MD King Wu via AMBER

Last message date: Fri Jun 30 2023 - 13:30:02 PDT
Archived on: Wed May 08 2024 - 05:56:03 PDT

Amber Archive Jun 2023 by date