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.

gromacswrapper

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

gmx-clusterbyfeatures

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

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.

streamd

Fully automated high-throughput MD pipeline

edrvis

A TUI for visualising GROMACS edr files.

vmd-hydrate-mcp

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

swarm-cg

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

pytim

a python package for the interfacial analysis of molecular simulations

novomcp

The open computational chemistry engine for drug discovery and materials science; MCP + REST + Workbench + Next.js dashboard, wrapping RDKit, GROMACS, AutoDock, OpenFold, Chai, Boltz, Gnina.

mdpow

Calculation of water/solvent partition coefficients with Gromacs.

lmp2gro

Converts LAMMPS data file into GROMACS input files

mdbenchmark

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

dnamd

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

pycgtool

Generate coarse-grained molecular dynamics models from atomistic trajectories.

nmrformd

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

gromacs-mcp

MCP server driving local GROMACS workflows for molecular dynamics setup, runs, and analysis.

lindemann

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

porems

Pore generator for molecular simulations.

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.

gmxpy

Wrapping GROMACS by python script for me

fretlabel

Nucleic acid fluorescence labeling for all-atom MD simulations

gromorg

A python GROMACS interface for MD simulations of organic molecular crystals