Top 75 molecular-dynamics open source projects

Tensorflow + Molecules = TensorMol

🚂 Python API for Emma's Markov Model Algorithms 🚂

The chemistry library you were waiting for

Development version of plumed 2

pyiron - an integrated development environment (IDE) for computational materials science.

Variational Autoencoder for Dimensionality Reduction of Time-Series

Molecular dynamics and Monte Carlo soft matter simulation on GPUs.

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

The ESPResSo package

Notebook-integrated tools for molecular simulation and visualization

Universal extensible molecular simulation engine

Powerful, efficient particle trajectory analysis in scientific Python.

🏗 Statistical models for biomolecular dynamics 🏗

GromacsWrapper is a python package that wraps system calls to Gromacs tools into thin classes. This allows for fairly seamless integration of the gromacs tools (v4.6.x, v5.x, 2016.x, 2018.x, 2019.x, all with the same Python code) into python scripts.

End-To-End Molecular Dynamics (MD) Engine using PyTorch

An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.

Collective variables module for molecular simulation and analysis programs

Molecular simulation in Julia

LOOS: a lightweight object-oriented structure analysis library

[email protected] COVID-19 efforts

the simple alchemistry library

Monte Carlo and Molecular Dynamics Simulation Package

Public development project of the LAMMPS MD software package

a python package for the interfacial analysis of molecular simulations

Unsupervised learning of atomic scale dynamics from molecular dynamics.

Qball (also known as [email protected]) is a first-principles molecular dynamics code that is used to compute the electronic structure of atoms, molecules, solids, and liquids within the Density Functional Theory (DFT) formalism. It is a fork of the Qbox code by Francois Gygi.

A CUDA project for Molecular Dynamics, Brownian Dynamics, Hydrodynamics... intended to simulate a very generic system constructing a simulation with modules.

A plugin that allows the use of Tensorflow in Hoomd-Blue for GPU-accelerated ML+MD

Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations

OpenMM is a toolkit for molecular simulation using high performance GPU code.

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

A curated list of Python packages related to chemistry

An open library for the analysis of molecular dynamics trajectories

SchNetPack - Deep Neural Networks for Atomistic Systems

HOOMD-blue example scripts.

In silico chemical library engine for high-accuracy chemical property prediction

ls1-MarDyn is a massively parallel Molecular Dynamics (MD) code for large systems. Its main target is the simulation of thermodynamics and nanofluidics. ls1-MarDyn is designed with a focus on performance and easy extensibility.

A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.

How to analyze molecular dynamics data with PyEMMA

Tinker: Software Tools for Molecular Design

RXMD : Linear-Scaling Parallel Reactive Molecular Dynamics Simulation Engine

Python interface of cpptraj

Tinker9: Next Generation of Tinker with GPU Support

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

Experiments with expanded ensembles to explore chemical space

UF3: a python library for generating ultra-fast interatomic potentials

Enables computations over a set of particles in N-dimensional space

MDToolbox.jl: A Julia package for molecular dynamics trajectories analysis and modeling of biomolecules

MolSSI SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store

The source of the votca-csg and xtp packages

Teaching Utility for Classical Atomistic Simulation.

quantum-dynamics-hub.github.io/libra/index.html

A script to build reference datasets for training neural network potentials from given LAMMPS trajectories.

sGDML - Reference implementation of the Symmetric Gradient Domain Machine Learning model

HMM implementation featuring Deal.II (FE) and LAMMPS (MD)

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

A hierarchical, component based molecule builder

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

High-performance operations for neural network potentials