Gromacs Python Packages

acpype

OFFICIAL: AnteChamber PYthon Parser interfacE

gromacswrapper

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

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:

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.

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

mdpow

A library for computing solvation/water partitioning coefficients using molecular dynamics simulations

mdbenchmark

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

dnamd

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

gromorg

Simple Gromacs python wrapper

pytim

Python Tool for Interfacial Molecules Analysis

lindemann

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

porems

Pore generator for molecular simulations.

streamd

Fully automated high-throughput MD pipeline

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.

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

PyMOL plugin to interactively label nucleic acids with fluorophores in silico