A collection of scripts and software to assist with biomolecular simulation in our laboratory
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Updated
Jan 30, 2018 - Shell
A collection of scripts and software to assist with biomolecular simulation in our laboratory
Shell scripts to run and extract output from GROMACS benchmarks.
GROMACS implementation of PVDF/CNT FF. PVDF from Sahihi et al. , J. Phys. Chem. C 2021 125 (39), 21635-21644, DOI: 10.1021/acs.jpcc.1c05894. CNT from OPLS-AA.
A gromacs tutorial for creating a gromos54A7 simulation system of a protein in a simple membrane
Simulate interactions between two fully-charged PAA chains with varying amounts of CaCl2 added
A collection of tutorials for running MD simulations using GROMACS.
Open source molecular dynamics analysis tools for GROMACS
Fast estimation of ion-pairing for screening electrolytes
This repository provide a automated method for Umbrella Sampling simulations to calculate binding energy between receptor and ligand.
Transfer Li ions from cathode to anode in MD simulations
Shell script to prepare protein PDBs for GROMACS molecular dynamics simulations, with SLURM script included to run md with hpc
This bash script requires gromacs and python installed on your system.
Bash shell scripts that process GROMACS files for automating a series of molecular-dynamics (MD) simulations on NERSC supercomputer.
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