A collection of tutorials for running MD simulations using GROMACS.
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Updated
Apr 15, 2021 - Shell
Molecular dynamics allows the atoms and molecules to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system.
A collection of tutorials for running MD simulations using GROMACS.
A collection of scripts and software to assist with biomolecular simulation in our laboratory
PaCS-MD (Parallel cascade selection molecular dynamics)
Scripts for analysing MD simulations of nanopores and DNA translocation (ionic current, translocation rate, pore hydrophobicity).
Generate soft matter blends via simulated solvent evaporation
Open source molecular dynamics analysis tools for GROMACS
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
WESTPA modified scripts with NAMD
Predicted and Experimental NMR Chemical Shifts at Variable Temperatures: The Effect of Protein Conformational Dynamics
Shell script to prepare protein PDBs for GROMACS molecular dynamics simulations, with SLURM script included to run md with hpc
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 script to automatically convert OMara group simulation datasets into a format suitable for the Australasian Computational and Simulation Commons data repository
Simulate interactions between two fully-charged PAA chains with varying amounts of CaCl2 added
Polymerize Atomistic P3HT
A gromacs tutorial for creating a gromos54A7 simulation system of a protein in a simple membrane
Scripts related to the Large-scale Atomic Molecular Massively Parallel Simulator