OFFICIAL: AnteChamber PYthon Parser interfacE

a python package for the interfacial analysis of molecular simulations

Framework for the rapid modeling glycans and glycoproteins.

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.

Membrane protein builder and parameterizer

Self explained tutorial for molecular dynamics simulation using gromacs

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

A Package for Parametrization of Molecular Mechanics Force Fields

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.

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

Automatic CHARMM-GUI browser interaction with Python

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.

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

Parametrize a LAMMPS data file with a CHARMM force field

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

Files used for the results presented in my physics undergraduate thesis.

xBFreE is a powerful and versatile tool for computing the Binding Free Energies using a variety of methods across popular Molecular Dynamics programs

Perform molecular dynamics experiments (MD) with NAMD on colab

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

CHARMM and X-PLOR binary trajectory file parser in Ruby