Scripts related to the Large-scale Atomic Molecular Massively Parallel Simulator
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Updated
Nov 9, 2019 - 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.
Scripts related to the Large-scale Atomic Molecular Massively Parallel Simulator
Generate good-looking images and movies with VMD
Simulate interactions between two fully-charged PAA chains with varying amounts of CaCl2 added
Predicted and Experimental NMR Chemical Shifts at Variable Temperatures: The Effect of Protein Conformational Dynamics
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
Polymerize Atomistic P3HT
A gromacs tutorial for creating a gromos54A7 simulation system of a protein in a simple membrane
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)
Open source molecular dynamics analysis tools for GROMACS
Scripts for analysing MD simulations of nanopores and DNA translocation (ionic current, translocation rate, pore hydrophobicity).
WESTPA modified scripts with NAMD
Shell script to prepare protein PDBs for GROMACS molecular dynamics simulations, with SLURM script included to run md with hpc
Transfer Li ions from cathode to anode in MD simulations
Generate soft matter blends via simulated solvent evaporation