79 Open source projects that are alternatives of or similar to mbuild

Physical validation of molecular simulations

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

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

[email protected] COVID-19 efforts

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

Folding@home GPU benchmark

Weighted Ensemble simulation framework in Python

a python package for the interfacial analysis of molecular simulations

Development version of plumed 2

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

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

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.

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

Molecular simulation in Julia

Modeling molecular ensembles with scalable data structures and parallel computing

Monte Carlo and Molecular Dynamics Simulation Package

🚂 Python API for Emma's Markov Model Algorithms 🚂

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.

Quantum mechanic mass spectrometry calculation program

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

Variational Autoencoder for Dimensionality Reduction of Time-Series

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

An open library for the analysis of molecular dynamics trajectories

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

HOOMD-blue example scripts.

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.

🏗 Statistical models for biomolecular dynamics 🏗

Tool to build force field input files for molecular simulation.

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

Packmol - Initial configurations for molecular dynamics simulations

Collective variables module for molecular simulation and analysis programs

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

LOOS: a lightweight object-oriented structure analysis library

Pytorch differentiable molecular dynamics

the simple alchemistry library

Tensorflow + Molecules = TensorMol

Public development project of the LAMMPS MD software package

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

Unsupervised learning of atomic scale dynamics from molecular dynamics.

The chemistry library you were waiting for

High-performance operations for neural network potentials

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

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

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

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

A curated list of Python packages related to chemistry

Molecular dynamics and Monte Carlo soft matter simulation on GPUs.

SchNetPack - Deep Neural Networks for Atomistic Systems

A toolkit for painting agent-based mesoscale molecular simulations and illustrations.

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

The ESPResSo package

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

Notebook-integrated tools for molecular simulation and visualization

How to analyze molecular dynamics data with PyEMMA

Universal extensible molecular simulation engine

Tinker: Software Tools for Molecular Design

Contact map analysis for biomolecules; based on MDTraj

Cassandra is a Monte Carlo package to conduct atomistic simulations.

Molecular dynamics simulation software