Amber Archive Jun 2023 by subject
- [AMBER] [Sender Not Verified] About polar solvation term in MMGBSA decomposition results
- [AMBER] [Sender Not Verified] Atom musk selection error
- [AMBER] [Sender Not Verified] Determine whether water molecules are with 1 Å of crystal waters from the PDB structure during the MD simulation
- [AMBER] [Sender Not Verified] Problems with minimization energy NaN
- [AMBER] [Sender Not Verified] Regarding Determination of HIS Residue States
- [AMBER] [Sender Not Verified] RNA with 5' phosphates
- [AMBER] [Sender Not Verified] Running gas phase TI with pmemd.CUDA.
- [AMBER] A script to build Amber on a Cray EX supercomputer with AMD GPU support
- [AMBER] About polar solvation term in MMGBSA decomposition results
- [AMBER] amber 22 installation
- [AMBER] AMBER calculation limitatation
- [AMBER] Amber22/Tools23 M2 Mac installation
- [AMBER] AMD GPU install problems
- [AMBER] AMD GPU install problems (David A Case)
- [AMBER] an-initio folding simulation
- [AMBER] Atom musk selection error
- [AMBER] Atom selection in cpptraj
- [AMBER] Can L4 GPU cards be used with AMBER 22?
- [AMBER] closest command cpptraj
- [AMBER] Cluster size
- [AMBER] Compiling Amber 22 (+ AT 23) with Intel compiler
- [AMBER] Compiling amber/Tools22 in Ubuntu 22.04
- [AMBER] Constant pH remd in amber
- [AMBER] Contant pH REMD run in amber22 using pmemd.cuda.MPI
- [AMBER] Correct interpretation of mmgbsa decomposition results
- [AMBER] cpptraj and nastruct
- [AMBER] Determine whether water molecules are with 1 Å of crystal waters from the PDB structure during the MD simulation
- [AMBER] Diffusion in pmemd.cuda
- [AMBER] electric field availability in the CUDA code
- [AMBER] Electrostatic potential calculation of the active site
- [AMBER] Energy bumps and structure deformation while minimization of a small molecule
- [AMBER] error in amber installation with cuda 9.0
- [AMBER] error in amber22 installation
- [AMBER] Error in modelling with ion using MCPB.py
- [AMBER] Error in running mmpbsa and mmgbsa
- [AMBER] Error while running mmpbsa
- [AMBER] ff19SB on Gromacs
- [AMBER] Fwd: [Sender Not Verified] Electrostatic potential calculation of the active site
- [AMBER] group pdb in clusters
- [AMBER] H-bond analysis in cpptraj
- [AMBER] huge memory consumption when running nab simulations
- [AMBER] Issue about atomic forces acting on each atom
- [AMBER] kerror about mmpbsa
- [AMBER] Keyerror about mmpbsa
- [AMBER] MCPB.py returns "ZeroDivisionError: float division by zero" in step 2
- [AMBER] Mix solvent MD
- [AMBER] Modified nucleic acid parameters
- [AMBER] Native contacts analysis in CPPTRAJ
- [AMBER] OPC vs. TIP3P
- [AMBER] Probability of Contact Formation
- [AMBER] Problems with minimization energy NaN
- [AMBER] qm/mmpbsa calculations
- [AMBER] Radii doubt during MCPB.py parametrization
- [AMBER] Regarding Determination of HIS Residue States
- [AMBER] Regarding K-means clustering
- [AMBER] RNA with 5' phosphates
- [AMBER] Rotational PMF Question
- [AMBER] Running gas phase TI with pmemd.CUDA.
- [AMBER] Self Inconsistency within antechamber for NAD and NAP cofactors (expects different bond orders in different routines)
- [AMBER] Serial Installation: 26 errors detected in the compilation of "/software/Amber22AmberTools23/amber22_src/src/pmemd/src/xray/cuda/src/xray/BulkMaskGPU.cu".
- [AMBER] Simulation protocol for Ionic Liquid (IL) - Bilayer system
- [AMBER] Tolerance problem in umbrella sampling
- [AMBER] Trouble Installing OpenMPI on Amazon Linux 2 (Centos)
- [AMBER] umbrella sampling
- [AMBER] unsuscribe
- [AMBER] Using plumed with amber
- [AMBER] 回复: cpptraj and nastruct
- [AMBER] 回复: Issue about atomic forces acting on each atom
- [AMBER] 回复: Keyerror about mmpbsa
- [AMBER] 回复: Using plumed with amber
- [AMBER] 回复: 回复: Issue about atomic forces acting on each atom
- [Sender Not Verified] Determine whether water molecules are with 1 Å of crystal waters from the PDB structure during the MD simulation
- Issues with simulating 5'-phosphorylated RNA strands
- Last message date: Fri Jun 30 2023 - 13:30:02 PDT
- Archived on: Wed Dec 11 2024 - 05:56:06 PST