/tools

The openmm-transformer repository simplifies the management of custom forces in OpenMM simulations, specifically focusing on the Buckingham nonbonded force. It allows users to easily prepare force field files for molecular dynamics simulations.

SILVIA is a project that models the synthesis of silica materials through multiscale computer simulations using the MARTINI coarse-grained forcefield. It allows for the simulation of silica condensation and the formation of silica mesophases in various conditions, demonstrating its applicability to molecular dynamics.

The ff-conversion-openmm repository is a utility designed to convert force field parameters from Tinker, LAMMPS, and Antechamber into OpenMM XML format. This tool facilitates the use of various force fields in molecular dynamics simulations using OpenMM.

PREMSO-2022 provides source code and configuration files for determining Lennard-Jones parameters using a surrogate-assisted global optimization approach. It integrates with Gromacs for molecular simulations and includes optimization algorithms for enhancing molecular modeling.

This repository provides a molecular force field for thiocyanate anions in water and at interfaces, along with Jupyter Notebooks for analyzing simulation data and performing molecular dynamics simulations. It includes tools for both classical and quantum-chemical calculations, making it useful for studying molecular interactions and properties.

ffconv is a Python tool designed to convert between different force-field topology file formats used in molecular simulations. It supports various formats and includes scripts to verify the accuracy of the conversions by comparing potential energies before and after the process.

The parmhess repository provides analytical Hessian fitting schemes aimed at improving parameterization in computational chemistry. This tool is particularly useful for researchers working on molecular simulations and dynamics, as it aids in the development of accurate force fields.

QCell is a collection of 525k quantum-mechanical calculations for diverse biomolecular fragments, including nucleic acids, lipids, and carbohydrates. It serves as a practical resource for training and benchmarking machine learning force fields, facilitating advancements in computational chemistry.

The 'topo-ff' tool is designed to parametrize LAMMPS data files using the CHARMM force field, facilitating molecular dynamics simulations. It aids in preparing molecular systems for computational studies by ensuring proper force field parameters are applied.

Sensitivity Analysis is a tool designed for optimizing force fields by computing the derivatives of the standard chemical potential with respect to van der Waals parameters. It aids in analyzing binding thermodynamics through simulations, making it useful for molecular dynamics studies.

This repository implements a rapid artificial neural network (RANN) derived interatomic potential for use in the LAMMPS molecular dynamics package. It aims to improve the speed and accuracy of molecular simulations by utilizing machine learning techniques to represent interatomic interactions.

This repository contains a script designed to automate the execution of the 'Lysozyme in Water' tutorial using GROMACS with multiple force fields. It facilitates molecular dynamics simulations by allowing users to easily run simulations with different parameters and force fields.

The 'plot_potential' repository allows users to plot individual potential functions that are part of force fields used in molecular simulations. It includes various energy terms such as harmonic bonds, van der Waals interactions, and electrostatics, making it useful for visualizing and understanding molecular dynamics.

MolecularDynamics is a JavaScript implementation of the ReaxFF reactive force field, designed for simulating hydrocarbon oxidation. It provides tools for molecular dynamics simulations, allowing users to visualize and interact with molecular structures and dynamics.

ReaxFF-nn is a machine learning potential that combines neural networks with the ReaxFF reactive force field to compute molecular interactions. It is implemented in the GULP package, allowing for advanced molecular simulations and calculations of properties like thermal conductivity in carbon nanostructures.

torchANI2Gaussian contains scripts that facilitate the integration of the TorchANI deep learning framework with the Gaussian quantum chemistry software. This allows users to leverage machine learning for molecular property predictions and simulations.

The ChIMES generator is a tool designed to develop parameter sets for molecular simulations, specifically within the framework of computational chemistry. It facilitates the creation and optimization of molecular models, making it useful for researchers in the field.

The 'cosm_scripts' repository contains force field parameters and scripts designed for modeling coarse-grained DNA origami structures. It supports molecular dynamics simulations and provides supplementary tools for researchers in the field of molecular modeling.

CapacMD is a molecular dynamics simulation code that utilizes a capacitance-polarizability force field to model charge migration and its effects on structural dynamics. It allows for the simulation of various molecular systems, including nanoparticles in different environments.

The MoSDeF + TraPPE repository provides tools for building and parameterizing molecular systems suitable for various simulation engines using the TraPPE force field. It includes implementation details for molecular dynamics simulations, making it relevant for computational chemistry applications.

K-G and Meatballs (KGMB) is a tool designed to facilitate the setup of molecular dynamics simulations for polymer composites. It generates starting configurations and LAMMPS input files using the Kremer-Grest coarse-grained force field, allowing for the simulation of polymer strands and filler particles.

This repository contains scripts for conducting a benchmark study on alchemical protein-ligand binding free energy calculations using the Perses and espaloma force fields. It compares the accuracy of different force fields against a custom protein-ligand benchmark dataset.

EmpiricalPotentials.jl is a Julia package that implements various empirical interatomic potentials compatible with AtomsBase and AtomsCalculators. It currently includes potentials like Lennard-Jones and Morse, which are used in molecular simulations to model interactions between atoms.

This repository contains a project aimed at fitting bond and angle parameters using the SMEE method, with a focus on benchmarking quantum mechanics. It involves creating and saving force field and topology inputs for molecular simulations.