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Molecular Dynamics Python Packages

Python packages with the GitHub topic molecular-dynamics. Sorted by relevance, with stars and monthly downloads.
mdanalysis
mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

463K 2K 832
mir-group
nequip

NequIP is a code for building E(3)-equivariant interatomic potentials

317K 910 210
mir-group
nequip-allegro

Allegro is an open-source code for building highly scalable and accurate equivariant deep learning interatomic potentials

299K 481 74
chemosim-lab
prolif

Interaction Fingerprints for protein-ligand complexes and more

146K 495 99
glotzerlab
freud-analysis

Powerful, efficient particle trajectory analysis in scientific Python.

94K 319 52
alchemistry
alchemlyb

the simple alchemistry library

82K 238 56
m3g
packmol

Packmol - Initial configurations for molecular dynamics simulations

36K 355 60
abhishektiwari
hbat

HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures

30K 8 2
mushroomfire
mdapy

A simple and fast python library to handle the data generated from molecular dynamics simulations

27K 97 13
alchemistry
alchemtest

the simple alchemistry test set

25K 10 13
metatensor
metatrain

Train, fine-tune, and manipulate machine learning models for atomistic systems

20K 68 27
bjmorgan
kinisi

A Python package for estimating diffusion properties from molecular dynamics simulations.

19K 84 15
N283T
zsasa

Fast SASA calculation using Zig

13K 0 0
deepmodeling
deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics

12K 2K 611
lab-cosmo
upet

Universal interatomic potentials for advanced materials modeling

10K 204 19
zincware
znh5md

ZnH5MD - High Performance Interface for H5MD Trajectories

8K 14 0
shirtsgroup
physical-validation

Physical validation of molecular simulations

8K 65 21
N283T
pyztraj

High-performance molecular dynamics trajectory analysis library in Zig

6K 0 0
mdanalysis
mdanalysistests

MDAnalysis is a Python library to analyze molecular dynamics simulations.

6K 2K 832
yesint
pymolar

Repository for molar crate and its dependencies

6K 51 3
openkim
kliff

KIM-based Learning-Integrated Fitting Framework for interatomic potentials.

5K 40 22
krisss0mecom
alphadynamics

Compact sequence-only neural propagator for protein torsion dynamics. 2.39x lower JSD than Microsoft Timewarp at 3000x fewer parameters. pip install alphadynamics.

5K 8 2
jewettaij
moltemplate

A general cross-platform tool for preparing simulations of molecules and complex molecular assemblies

5K 315 106
Becksteinlab
gromacswrapper

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

5K 190 54
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