gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

List of molecules (small molecules, RNA, peptide, protein, enzymes, antibody, and PPIs) conformations and molecular dynamics (force fields) using generative artificial intelligence and deep learning

OFFICIAL: AnteChamber PYthon Parser interfacE

Collective variables library for molecular simulation and analysis programs

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).

tools for GROMACS

a python package for the interfacial analysis of molecular simulations

Gromacs to Lammps simulation converter

Software Suite for Advanced General Ensemble Simulations

Fully automated high-throughput MD pipeline

A project (and object) for storing, manipulating, and converting molecular mechanics data.

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

Generate coarse-grained molecular dynamics models from atomistic trajectories.

The source of the votca-csg and xtp packages

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

Full automation of relative protein-ligand binding free energy calculations in GROMACS

Google Colab notebooks for running molecular dynamics simulations with GROMACS

molecular dynamics simulation and analysis. 分子动力学模拟和分析。

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.

Web Platform made with Python and NextJS for automating GROMACS simulations

Force Distribution Analysis (FDA) for GROMACS

Conversion of coarsegrain to atomistic (complete rewrite of the original CG2AT)

Calculation of water/solvent partition coefficients with Gromacs.

To analyze fluctuations in DNA or RNA structures in molecular dynamics trajectories.

Generate PEG topology for GROMACS and LAMMPS

NMRforMD is a python script for the calculation of NMR relaxation time T1 and T2 from molecular dynamics trajectory file.

lindemann is a python package to calculate the Lindemann index of a lammps trajectory

For the purpose of post progressing of MD carried by gromacs

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

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