/tools

LAMMPS is a classical molecular dynamics simulation code that efficiently runs on parallel computers. It is used for simulating a wide range of molecular systems, including small molecules and proteins, and is maintained as an open-source project.

FAIR Chemistry's `fairchem` library offers a centralized repository of machine learning models and methods tailored for chemistry and materials science. It supports various tasks such as predicting molecular properties, running molecular dynamics simulations, and optimizing molecular structures.

DeePMD-kit is a deep learning package designed to create models for interatomic potential energy and perform molecular dynamics simulations. It interfaces with various deep learning frameworks and classical molecular dynamics packages, making it suitable for a wide range of molecular systems.

OpenMM is a high-performance toolkit for molecular simulation that utilizes GPU acceleration. It provides flexibility and efficiency for running molecular dynamics simulations, making it a valuable resource for researchers in computational chemistry.

MDAnalysis is a Python library that facilitates the analysis of molecular dynamics simulations. It supports various simulation packages and provides algorithms for analyzing molecular interactions, making it a valuable tool for researchers in computational chemistry and molecular biology.

JAX MD is a library for accelerated and differentiable molecular dynamics simulations, allowing researchers to efficiently simulate molecular systems and compute energies and forces. It leverages JAX for hardware acceleration and automatic differentiation, making it suitable for advanced molecular simulations and experiments.

MolecularNodes is an add-on for Blender that facilitates the import and visualization of structural biology data. It allows users to create animations from molecular structures and import molecular dynamics trajectories, enhancing the representation of proteins and other molecules.

This repository contains input files and datasets for the Folding@home efforts to understand and target the SARS-CoV-2 virus with small molecule and antibody therapeutics. It supports molecular dynamics simulations and provides resources for researchers working on COVID-19 related molecular studies.

CP2K is a quantum chemistry and solid state physics software package that enables atomistic simulations of various systems, including molecular and biological ones. It supports multiple modeling methods and can perform simulations such as molecular dynamics, energy minimization, and transition state optimization.

SchNetPack is a toolbox that facilitates the development and application of deep neural networks for predicting quantum-chemical properties and potential energy surfaces of molecules and materials. It includes features for training models on benchmark datasets and supports molecular dynamics simulations, making it a comprehensive tool for atomistic machine learning.

GROMACS is a powerful molecular simulation toolkit that allows users to perform molecular dynamics simulations efficiently. It is widely used in the field of computational chemistry for studying the behavior of biomolecules and materials at the atomic level.

NequIP is an open-source framework for constructing E(3)-equivariant interatomic potentials, enabling accurate molecular simulations. It supports multi-GPU training and integrates with existing molecular dynamics software, making it a valuable tool for researchers in computational chemistry and materials science.

Dynamic PDB is a large-scale dataset that integrates dynamic behaviors and physical properties in protein structures, enhancing existing protein databases. It includes data from all-atom molecular dynamics simulations, capturing conformational changes and various physical attributes of proteins.

BioEmu is a tool that emulates protein equilibrium ensembles by sampling structures based on amino acid sequences using generative deep learning techniques. It includes features for steering samples towards physically plausible conformations and can be used for side-chain reconstruction and molecular dynamics equilibration.

GPUMD is a highly efficient molecular dynamics package designed for GPU acceleration. It supports the training and application of neuroevolution potentials, enabling advanced atomistic simulations for various materials.

MDTraj is an open-source Python library that allows users to read, write, and analyze molecular dynamics trajectories. It supports a wide variety of file formats and provides fast analysis functions, making it a valuable tool for researchers in molecular dynamics and computational chemistry.

TorchMD is an end-to-end molecular dynamics engine that leverages PyTorch to facilitate molecular simulations. It provides a user-friendly API for researchers to conduct force-field development and integrate neural network potentials into molecular dynamics workflows.

PDBFixer is an application that addresses common issues in Protein Data Bank files, such as adding missing atoms and building loops, to facilitate their use in molecular simulations. It streamlines the preparation of protein structures for further computational analysis.

NWChem is an open-source software package designed for high-performance computational chemistry. It provides tools for electronic structure calculations and molecular simulations, enabling researchers to study molecular properties and dynamics effectively.

AI2BMD is a program designed for efficient ab initio biomolecular dynamics simulations of proteins. It includes capabilities for simulating molecular dynamics, preprocessing protein structures, and provides datasets for training molecular models.

TorchANI 2.0 is an open-source library that facilitates the training and application of ANI-style neural network interatomic potentials. It supports molecular dynamics simulations and is designed for high-performance computation in quantum chemistry, making it a valuable tool for researchers in the field.

The 'orb-models' repository offers pretrained forcefield models designed for atomic simulations, enabling users to predict molecular properties and perform molecular dynamics simulations. It supports various molecular systems, including metal complexes and biomolecules, and allows for fine-tuning with custom datasets.

AlphaFlow is a modified version of AlphaFold that employs flow matching to generate protein conformational ensembles. It is capable of modeling both experimental and molecular dynamics ensembles, providing tools for protein design and simulation.

PLUMED 2 is a plugin for molecular dynamics simulations that enables enhanced sampling and free energy calculations. It provides tools for trajectory analysis and is widely used in computational chemistry to study molecular systems.