/tools

Grappa is a machine learned molecular mechanics force field that utilizes graph neural networks to predict bonded parameters for molecular simulations. It integrates with GROMACS and OpenMM, allowing users to parametrize systems and train custom models using various molecular datasets.

The 'cgdms' repository provides a Python package for differentiable molecular simulation of proteins using a coarse-grained potential. It includes functionalities for simulating protein dynamics, calculating energies, and designing proteins based on learned potentials.

RMD_Digging is a toolkit designed for pre-processing and post-processing tasks in reactive molecular dynamics simulations using the ReaxFF force field. It includes functionalities for data extraction, statistical analysis, and visualization of molecular structures and trajectories.

This repository contains models for spectral neighbor analysis potential (SNAP) used in molecular simulations. It includes force field parameters and training data, facilitating the development and application of these models in computational chemistry.

flare++ is a software tool that extends the FLARE code to implement Bayesian force fields using sparse Gaussian process regression. It is designed for efficient molecular dynamics simulations and includes features for training force fields based on energy and force data.

I-ReaxFF is a differentiable framework for the Reactive Force Field (ReaxFF) based on TensorFlow, allowing for the optimization of ReaxFF parameters using machine learning techniques. It facilitates molecular simulations by providing first and higher-order derivatives of energies, which are essential for various computational chemistry applications.

OPLSAA-DB is a database containing hand-built OPLS-AA parameters and topologies for 464 molecules, facilitating molecular simulations across various platforms such as OpenMM, Gromacs, and NAMD. It serves as a resource for researchers working on molecular dynamics and simulations in computational chemistry.

The ccpbiosim-2023 repository provides educational materials for a workshop on molecular simulations and force fields, including notebooks for working with protein-ligand systems and other molecular types. It serves as a tutorial resource for users interested in molecular modeling and simulation techniques.

This repository contains Python scripts for conducting GPU-accelerated molecular dynamics simulations with the AMOEBA force field, specifically tailored for simulating ion channels and other biomolecules. It enhances OpenMM's capabilities with features for system preparation, trajectory conversion, and umbrella sampling simulations.

GPUGA is a tool designed for empirical potential fitting using a genetic algorithm, optimized for GPU performance. It allows for efficient modeling of molecular interactions, particularly in the context of materials like diamond silicon.

PEGgenerator is a tool designed to generate PEG topology for molecular dynamics simulations in GROMACS and LAMMPS. It allows users to create configurations for PEG molecules with varying numbers of monomers and perform energy minimization and relaxation simulations.

The ChIMES calculator provides a flexible toolset for evaluating interactions using the Chebyshev Interaction Model for Efficient Simulation (ChIMES), which is a machine-learned interatomic potential. It is applicable in various molecular simulations and can be integrated into other codes for advanced computational chemistry tasks.

LigParGen is a repository that provides tutorials and FAQs about the LigParGen Server, which is used for generating ligand parameters for molecular dynamics simulations. It focuses on the application of force fields in molecular simulations.

The cnt-gaff repository contains tools for building atomistic structures of carbon nanotubes and assigning generalized Amber force field parameters. It includes scripts for generating CNTs with functional groups and setting up simulations for molecular dynamics studies.

The PTM Parameterization Prototype allows users to parameterize proteins with post-translational modifications and simulate them using the OpenFF Rosemary force field. It provides a Jupyter Notebook that demonstrates how to handle both canonical and non-canonical amino acids in protein simulations.

Torsionfit is a toolkit designed for Bayesian parameterization of torsion angles in molecular mechanics forcefields, utilizing quantum chemical data. It aims to improve the accuracy of molecular simulations by refining torsion parameters based on statistical inference methods.

Ichor is a Python package designed to simplify data management from computational chemistry programs and support machine learning force field development. It provides interfaces for various computational chemistry software, flexible data structures for managing large datasets, and tools for benchmarking molecular dynamics simulations.

This repository provides a Python code for simulating the Brownian motion of colloidal particles under the influence of a time-varying force field. It is particularly useful for applications in microfluidics and lab-on-a-chip technologies, allowing for the analysis of particle trajectories and interactions in various force environments.

The 'tutorial-lmp' repository offers step-by-step instructions for setting up and running molecular dynamics simulations with polarizable force fields in LAMMPS. It covers the creation of simulation boxes, equilibration, and the addition of explicit polarization terms, making it a valuable resource for those interested in molecular simulations.

The OpenMM XTB plugin allows users to compute molecular forces and energies using the XTB quantum chemistry methods. It integrates with OpenMM to facilitate molecular dynamics simulations, enabling the use of advanced quantum mechanical calculations in a molecular simulation framework.

Open3SPN2 is an implementation of the 3SPN2 and 3SPN2.C coarse-grained molecular models of DNA designed for use with OpenMM. It facilitates molecular simulations and dynamics, particularly focusing on DNA and its interactions with proteins.

MSIBI is a Python package designed for managing and running coarse-grain potential optimizations through the MultiState Iterative Boltzmann Inversion method. It facilitates the optimization of both intra-molecular and inter-molecular potentials, making it a valuable tool for molecular dynamics simulations.

LigParGen-CommandFiles provides the necessary command files to install LigParGen locally, a tool used for generating force fields for ligands in molecular dynamics simulations. This repository supports the computational chemistry community by facilitating the setup of simulations involving small molecules.

PhyNEO is a hybrid force field development workflow that enhances traditional physics-based methods with neural networks to achieve accurate molecular simulations. It focuses on generating force fields for organic molecules and polymers, facilitating molecular dynamics simulations and analysis of properties like conductivity and diffusion coefficients.