Collective variables library for molecular simulation and analysis programs

a python package for the interfacial analysis of molecular simulations

Quickly generate, start and analyze benchmarks for molecular dynamics simulations.

Database of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Gromacs, NAMD, CHARMM, LAMMPS, TINKER, CNS/X-PLOR, Q, DESMOND, BOSS and MCPRO.

Longbow is a tool for automating simulations on a remote HPC machine. Longbow is designed to mimic the normal way an application is run locally but allows simulations to be sent to powerful machines.

Package to perform minimum-distance distribution analyses of complex solute-solvent interactions

PaCS-Toolkit: Optimized software utilities for PaCS-MD and following analysis

NAMD-xtb-QMMM-interface

A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD

TcL/VMD/psfgen/bash scripts for generating MD systems for use with NAMD

Using VMD and NAMD for molecular dynamics simulation of protein PDB files.

Tutorial for converting NAMD psf/pdb files to CHARMM PSF/CRD (credit attributed where appropriate to the AMAZING humans who developed these scripts)

A simple collective-variables module for NAMD via tclforces; implements TAMD

All GROMACS/NAMD initializing files for generating initial structures for polydisperse chains with a set of residues desired by the user. With LigninBuilder, all lignin topologies can be built directly.

Gromacs that can be accelerated at AMD GPU

a VScode syntax highlight tool for molecular dynamics

Scripts useful for running NAMD simulations

study of external electric fields' effects on the tubulin dimer via MD

FabMD is a FabSim3 plugin for automated LAMMPS-based simulations.

Scripts used for analysis of various systems and the pertaining variables or reaction coordinates