physical_validation — Peer-reviewed • Rank 11.8 • Science 98%

physical_validation: A Python package to assess the physical validity of molecular simulation results - Published in JOSS (2022)

foyer • Rank 14.7 • Science 77%

A package for atom-typing as well as applying and disseminating forcefields

openff-interchange • Rank 10.0 • Science 77%

A project (and object) for storing, manipulating, and converting molecular mechanics data.

mbuild • Rank 15.8 • Science 67%

A hierarchical, component based molecule builder

Molly • Rank 12.5 • Science 67%

Molecular simulation in Julia

mbgdml • Rank 3.0 • Science 75%

Create, use, and analyze machine learning potentials within the many-body expansion framework.

torchani • Rank 17.2 • Science 59%

Accurate Neural Network Potential on PyTorch

mdanalysis • Rank 24.5 • Science 49%

MDAnalysis is a Python library to analyze molecular dynamics simulations.

nlesc-flamingo • Rank 6.0 • Science 64%

Computation and filtering of molecular properties

transfer_li • Rank 2.5 • Science 67%

Transfer Li ions from cathode to anode in MD simulations

westpa • Rank 15.1 • Science 54%

WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis

lintf2_ether_ana_postproc • Rank 1.8 • Science 67%

Analysis postprocessing utilities for my molecular dynamics simulations of LiTFSI-Ether mixtures

deerpredict • Rank 8.2 • Science 57%

Software for the prediction of DEER and PRE data from conformational ensembles.

https://github.com/theochem/iodata • Rank 15.2 • Science 49%

Python library for reading, writing, and converting computational chemistry file formats and generating input files.

faunus • Rank 9.1 • Science 49%

A Framework for Metropolis Monte Carlo Simulation of Molecular Systems

rcbs.py • Rank 2.9 • Science 54%

RCBS.py (Reactivity of Chemical and Biochemical Systems) is a Python package that contains several scripts, functions and classes that simplify the analysis of chemical and biochemical simulations.

https://github.com/m3g/complexmixtures.jl • Rank 7.6 • Science 49%

Package to perform minimum-distance distribution analyses of complex solute-solvent interactions

molsysmt • Rank 4.7 • Science 49%

Open source library to work with molecular systems

tensormol • Rank 10.2 • Science 33%

Tensorflow + Molecules = TensorMol

moleculardymics • Rank 1.8 • Science 41%

This workflow for molecular dynamics simulation of proteins

AdaptivePELE • Rank 5.5 • Science 33%

AdaptivePELE is a Python package aimed at enhancing the sampling of molecular simulations

https://github.com/lumol-org/lumol • Rank 15.5 • Science 23%

Universal extensible molecular simulation engine

pose • Science 44%

A bare metal Python library for building and manipulating protein molecular structures

https://github.com/aqlaboratory/pnerf • Science 36%

https://github.com/cavenfish/yass.jl • Science 26%

Yet Another Simulation Suite (YASS.jl). A simulation suite for atomic simulations in Julia.

hs_alkane • Science 67%

Fortran2003 code (with C and Python bindings) implementing hard-sphere alkane models

YetAnotherSimulationSuite.jl: An Atomic Simulation Suite in Julia • Science 87%

YetAnotherSimulationSuite.jl: An Atomic Simulation Suite in Julia - Published in JOSS (2025)

particlesmc • Science 44%

Package to run atomic / molecular Monte Carlo simulations

scalar_codes • Science 57%

Codes for automating standard VASP and VASP-related calculations.

https://github.com/aiqm/aimnet • Science 13%

Atoms In Molecules Neural Network Potential

mdtools • Science 67%

Scripts to prepare and analyze molecular dynamics simulations