OFFICIAL: AnteChamber PYthon Parser interfacE

a python package for the interfacial analysis of molecular 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.

A Package for Parametrization of Molecular Mechanics Force Fields

Framework for the rapid modeling glycans and glycoproteins.

Self explained tutorial for molecular dynamics simulation using gromacs

Membrane protein builder and parameterizer

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.

Automatic CHARMM-GUI browser interaction with Python

This code adds custom-made amino acids to the GROMACS forcefield directory.

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

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

A multi-purpose tool for automated setup of MD systems (e.g. for transformato) and local, menu-based rerunning of CHARMM-GUI input scripts for CHARMM

CodeEntropy is a python package and a collection of scripts that can be used to compute entropy using the multiscale-cell-correlation (MCC) theory from MD simulations.

Parametrize a LAMMPS data file with a CHARMM force field

This repository provides the latest benchmarks for the CHARMM/pyCHARMM program on GPUs

Perform molecular dynamics experiments (MD) with NAMD on colab

VMD plug-in for building a peptide ab initio from backbone torsion angles or secondary structure

Just get me a topology, for god’s sake!

Comprehensive molecular dynamics simulations and drug design analysis for PTEN protein: workflows include protein dynamics, binding site detection, ligand screening, and filtering for therapeutic discovery.