Martini 3 small-molecule database

MACE-MP models

Self explained tutorial for molecular dynamics simulation using gromacs

Helping MD customers run workloads on Graviton 3E instances (especially hpc7g) with optimized compiler settings

This repository provide a automated method for Umbrella Sampling simulations to calculate binding energy between receptor and ligand.

Martini 3 small-molecule database

Prediction of magnesium binding sites in RNA molecules using GCMC/MD (Updated version: https://github.com/mackerell-lab/GCMC_PME)

Generate soft matter blends via simulated solvent evaporation

singularity definitions of GROMACS

Efficiently handle multiple simulations using bash

Scripts for analysing MD simulations of nanopores and DNA translocation (ionic current, translocation rate, pore hydrophobicity).

Transfer Li ions from cathode to anode in MD simulations

A collection of tutorials for running MD simulations using GROMACS.

PaCS-MD (Parallel cascade selection molecular dynamics)

A collection of scripts and software to assist with biomolecular simulation in our laboratory

Open source molecular dynamics analysis tools for GROMACS

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

Simulate interactions between two fully-charged PAA chains with varying amounts of CaCl2 added

Scripts related to the Large-scale Atomic Molecular Massively Parallel Simulator