160 Open source projects that are alternatives of or similar to nequip

RXMD : Linear-Scaling Parallel Reactive Molecular Dynamics Simulation Engine

Notebook-integrated tools for molecular simulation and visualization

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

Powerful, efficient particle trajectory analysis in scientific Python.

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

Tools, utility, parsers useful in daily material science work

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

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.

stda program for computing excited states and response functions via simplified TD-DFT methods (sTDA, sTD-DFT, and SF-sTD-DFT)

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

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

Molecular dynamics simulation software

Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.

A hierarchical, component based molecule builder

Molecular simulation in Julia

High-performance operations for neural network potentials

atomate2 is a library of computational materials science workflows

[email protected] COVID-19 efforts

SchNetPack - Deep Neural Networks for Atomistic Systems

Original implementation of Calibrated Boosting-Forest

Packmol - Initial configurations for molecular dynamics simulations

Fitting thermodynamic models with pycalphad - https://doi.org/10.1557/mrc.2019.59

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

Monte Carlo and Molecular Dynamics Simulation Package

Folding@home GPU benchmark

a python package for the interfacial analysis of molecular simulations

A curated list of resources for machine learning for small-molecule drug discovery

QUICK: A GPU-enabled ab intio quantum chemistry software package

Molecular dynamics and Monte Carlo soft matter simulation on GPUs.

code for Gogleva et al manuscript

Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

Quantum Package : a programming environment for wave function methods

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.

DeepChem 2017: Deep Learning & NLP for Computational Chemistry, Biology & Nano-materials

🚂 Python API for Emma's Markov Model Algorithms 🚂

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

Graph-based machine learning for chemical property prediction

Tool to build force field input files for molecular simulation.

Quantum Mechanical Bespoke Force Field Derivation Toolkit

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

DENOPTIM is a software package for de novo design and virtual screening of functional molecules of any kind.

Development version of plumed 2

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

RxDock is a fork of rDock. Note: the latest code is under development. Please do git checkout patched-rdock after clone if you want patched rDock. [IMPORTANT NOTE: pull requests should be posted on GitLab, this is a read-only source code mirror]

DMFTwDFT: An open-source code combining Dynamical Mean Field Theory with various Density Functional Theory packages

A PyTorch and TorchDrug based deep learning library for drug pair scoring.

An open library for the analysis of molecular dynamics trajectories

Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)

Variational Autoencoder for Dimensionality Reduction of Time-Series

Template with code & dataset for the "Structural basis for solubility in protein expression systems" challenge at the Copenhagen Bioinformatics Hackathon 2021.

HOOMD-blue example scripts.

odr.chalmers.se/handle/20.500.12380/256629?locale=en

Computational Analysis of Novel Drug Opportunities

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

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

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.

Physical validation of molecular simulations

Codes for text-mined solid-state reactions dataset

A Software to interactively edit data in a graphical manner

The ESPResSo package