76 Open source projects that are alternatives of or similar to MDToolbox.jl

🏗 Statistical models for biomolecular dynamics 🏗

the simple alchemistry library

Tool to build force field input files for molecular simulation.

The ESPResSo package

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

A Python library and command line interface for automated free energy calculations

Collective variables module for molecular simulation and analysis programs

High-performance operations for neural network potentials

Unsupervised learning of atomic scale dynamics from molecular dynamics.

Tensorflow + Molecules = TensorMol

Molecular dynamics and Monte Carlo soft matter simulation on GPUs.

A curated list of Python packages related to chemistry

Flexible implementation of cell lists to map the calculations of particle-pair dependent functions, such as forces, energies, neighbour lists, etc.

Universal extensible molecular simulation engine

A hierarchical, component based molecule builder

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

Physical validation of molecular simulations

LOOS: a lightweight object-oriented structure analysis library

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

Public development project of the LAMMPS MD software package

😎 A curated list of awesome Molecular Dynamics libraries, tools and software.

Pytorch differentiable molecular dynamics

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

The chemistry library you were waiting for

Variational Autoencoder for Dimensionality Reduction of Time-Series

An open library for the analysis of molecular dynamics trajectories

Modeling molecular ensembles with scalable data structures and parallel computing

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

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

Notebook-integrated tools for molecular simulation and visualization

Weighted Ensemble simulation framework in Python

Powerful, efficient particle trajectory analysis in scientific Python.

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

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.

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

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

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

Molecular simulation in Julia

Molecular dynamics simulation software

[email protected] COVID-19 efforts

The source of the votca-csg and xtp packages

Monte Carlo and Molecular Dynamics Simulation Package

Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMM

a python package for the interfacial analysis of molecular simulations

Contact map analysis for biomolecules; based on MDTraj

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.

Folding@home GPU benchmark

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

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

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

🚂 Python API for Emma's Markov Model Algorithms 🚂

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

Quantum mechanic mass spectrometry calculation program

Development version of plumed 2

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

Teaching Utility for Classical Atomistic Simulation.

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

Packmol - Initial configurations for molecular dynamics simulations

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