Gromacs Python Packages

acpype

OFFICIAL: AnteChamber PYthon Parser interfacE

gmx-mmpbsa

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

gmx-clusterbyfeatures

Features Based Conformational Clustering of MD trajectories. See details at:

gromacswrapper

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

lmp2gro

Converts LAMMPS data file into GROMACS input files

pytim

a python package for the interfacial analysis of molecular simulations

longbow

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.

vmd-hydrate-mcp

An MCP server that drives VMD for GROMACS/LAMMPS trajectory analysis + clathrate-hydrate cage science (requires a local VMD install)

mdbenchmark

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

swarm-cg

Tools for automatic parametrization of bonded terms in coarse-grained molecular models, with respect to an all-atom trajectory

dnamd

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

samgen

Build self-assembled monolayer (SAM) surfaces for GROMACS

mdpow

Calculation of water/solvent partition coefficients with Gromacs.

porems

Pore Generator for Molecular Simulations.

lindemann

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

nmrformd

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

pycgtool

Generate coarse-grained molecular dynamics models from atomistic trajectories.

gromorg

Simple Gromacs python wrapper

streamd

Streamd Python module to facilitate molecular dynamics

jlhpy

Contains input files and workflows underlying J. L. Hörmann, C. (刘宸旭) Liu, Y. (孟永钢) Meng, and L. Pastewka, “Molecular simulations of sliding on SDS surfactant films,” The Journal of Chemical Physics, vol. 158, no. 24, p. 244703, Jun. 2023, doi: 10.1063/5.0153397. as well as an installable Python package jlhpy.

fretlabel

PyMOL plugin to interactively label nucleic acids with fluorophores in silico

gmxpy

Wrapping GROMACS by Python for me