Differentiable molecular simulation of proteins with a coarse-grained potential

Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

⚡ general purpose coarse-grained molecular dynamics simulation package

Massively parallel hybrid particle-field molecular dynamics in Python.

Generate and perturb protein structural ensembles using the ExProSE algorithm

Object-Oriented Perl 5, Moose Library for Molecular Hacking

Massively parallel hybrid particle-field molecular dynamics (hPF-MD) simulation method in Julia

Tutorial examples for HylleraasMD

Molecular Dynamics Trajectory Analysis Tools

This repo consists of Monte Carlo C++ codes used to run coarse-grained simulations for biopolymers like DNA.

A toolkit for working with coarse-grain systems

Molecular simulator for proteins that uses Go-type potentials

Files required for our tutorial on PEGylated proteins

Force field parameters and supplementary scripts for the "A coarse-grained model for DNA origami" paper by R. Reshetnikov, A. Stolyarova, A. Zalevsky et. al.

Analyze two-component nanoparticle properties for classical molecular dynamics simulations

Simulating tumour development in two and three dimensions using the framework of the spatial Tangled Nature model