OFFICIAL: AnteChamber PYthon Parser interfacE

a python package for the interfacial analysis of molecular simulations

Self explained tutorial for molecular dynamics simulation using gromacs

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.

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.

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

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

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

⌨️ The CHARMM programming language IDE submodule for SNU Programming Tools (2D Mode)

Perform molecular dynamics experiments (MD) with NAMD on colab

📚️ A repository for showcasing my knowledge of the CHARMM programming language, and continuing to learn the language.

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

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

Setup, run and analyse Adaptive MDeNM simulations on CHARMM

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

CHARMM Parameter File Search Engine: A web-based application designed for parsing, viewing, and analyzing CHARMM parameter files. This tool offers an intuitive interface for researchers and developers, enabling efficient file management, interactive data visualization, and advanced search capabilities.

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

PEPDROID force field for peptoids

A lightweight, fast, and pure Rust library for the simple assignment of force field partial charges to proteins and nucleic acids. It provides a straightforward residue-and-atom-name mapping system supporting major force fields like AMBER and CHARMM, designed for performance-critical molecular modeling pipelines.

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.

Extract physical frames from a lambda-dynamics trajectory

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