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Gromacs Python Packages

Python packages with the GitHub topic gromacs. Sorted by relevance, with stars and monthly downloads.
alanwilter
acpype

OFFICIAL: AnteChamber PYthon Parser interfacE

5K 249 58
Becksteinlab
gromacswrapper

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

5K 190 54
Valdes-Tresanco-MS
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.

4K 305 85
rjdkmr
gmx-clusterbyfeatures

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

3K 10 3
HECBioSim
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.

1K 18 5
GMPavanLab
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

702 48 13
Becksteinlab
mdpow

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

582 29 10
bio-phys
mdbenchmark

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

495 83 17
rjdkmr
dnamd

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

384 30 10
abelcarreras
gromorg

Simple Gromacs python wrapper

378 4 2
Marcello-Sega
pytim

Python Tool for Interfacial Molecules Analysis

378 95 38
N720720
lindemann

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

310 24 5
Ajax23
porems

Pore generator for molecular simulations.

307 8 5
ci-lab-cz
streamd

Fully automated high-throughput MD pipeline

306 95 20
simongravelle
nmrformd

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

242 25 7
jag1g13
pycgtool

Generate coarse-grained molecular dynamics models from atomistic trajectories.

226 67 15
jotelha
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.

205 1 0
Goosang-Yu
gmxpy

Wrapping GROMACS by python script for me

202 2 1
RNA-FRETools
fretlabel

PyMOL plugin to interactively label nucleic acids with fluorophores in silico

193 5 2
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