/tools

CL&Pol is a tool designed for simulating polarisable force fields specifically for ionic liquids. It includes scripts for adding Drude induced dipoles, scaling Lennard-Jones interactions, and modifying force field parameters, making it useful for molecular dynamics simulations.

GAML is a Genetic Algorithm Machine Learning software package that automates the creation of force field parameters for molecular dynamics and Monte Carlo simulations. It emphasizes atomic charge development for solvent simulations and outputs files compatible with GROMACS, validating parameters against various physical properties.

gmx_ffconv is a semi-automated force field converter for GROMACS that allows users to convert molecular systems between different all-atom force fields. It requires topology files for the molecules and facilitates the conversion process without needing extensive programming knowledge.

Multi-eGO is a set of tools designed to generate a multi-eGO force field for performing molecular dynamics simulations. It facilitates the setup and analysis of simulations involving proteins and self-assembly processes.

This repository contains OPLS-AA force field parameters designed for simulating deep eutectic solvents. It includes a tutorial for constructing a simulation box and performing molecular dynamics simulations using these parameters.

Conformer-Search is a workflow designed for minimum energy conformer search of molecules using force field optimization methods like UFF and MMFF94. It allows users to import molecules from SMILES, generate conformers, optimize them, and select the minimum energy conformer for further analysis.

GA4AMOEBA is a genetic algorithm program designed to optimize parameters of the AMOEBA polarizable force field. It is intended for use in molecular simulations, particularly in high-performance computing environments.

The spica-tools repository offers tools for setting up coarse-grained molecular dynamics simulations using the SPICA force field. It includes functionalities for mapping all-atom configurations to coarse-grained representations and generating input files for popular molecular dynamics software like LAMMPS and GROMACS.

This repository contains a reaxFF LAMMPS script designed to simulate the oxidation of nanomaterials, followed by thermal equilibration and tensile testing. It aims to investigate how oxidation impacts the tensile strength of materials, making it relevant for studies in molecular dynamics and materials science.

The 'rev-sim' repository provides code and data for reversible molecular simulation aimed at training classical and machine learning force fields. It includes scripts for running simulations and benchmarks, making it useful for molecular dynamics and related computational chemistry tasks.

TorchMMFF94 provides a PyTorch implementation of the MMFF94 force field, enabling molecular energy minimization both in isolation and in the context of protein pockets. It offers a simple interface for testing and running examples related to molecular optimization.

The SMIRNOFF Plugins repository offers a framework for using custom functional forms in SMIRNOFF-based force fields, enabling researchers to parameterize molecular interactions for simulations. It includes various parameter handlers for different potential types, facilitating the modeling of molecular systems.

The xtbiff program is designed to implement a general intermolecular force field using tight-binding quantum chemical calculations. It can be utilized in molecular simulations and is compatible with other computational chemistry tools.

The 'topo-tools-scripts' repository provides scripts for preparing input files for molecular dynamics simulations of gases in MOF-74 analogues. It focuses on generating LAMMPS input files for simulating the adsorption of methane and carbon dioxide in metal-organic frameworks using a DFT-derived force field.

The addNewResidue.py script allows users to add custom-made amino acids to the GROMACS forcefield directory, supporting both AMBER and CHARMM forcefields. It facilitates the preparation of molecular simulations by enabling the incorporation of new residues into protein structures.

mbGDML is a tool for creating, using, and analyzing machine learning potentials within the many-body expansion framework. It allows for accurate predictions of molecular properties and supports molecular dynamics simulations, making it a valuable resource in computational chemistry.

LAMMPS-LMFF is an extension of the LAMMPS molecular dynamics package, designed to study layered materials like graphene and boron hexanitride. It includes optimizations for performance on supercomputers, enabling efficient simulations of large atomic systems.

This repository serves as a template for disseminating force fields using the Foyer library, allowing users to create and validate force field files for molecular dynamics simulations. It includes instructions for generating force fields and testing their syntax, making it a useful resource for researchers in computational chemistry.

YAMMBS is a benchmarking suite designed for evaluating molecular mechanics force fields. It allows users to run benchmarks on molecular structures and analyze the performance of different force fields in optimizing molecular geometries.

The 'generate-parameter-files' repository is a Python package designed to generate molecular potential files for use in LAMMPS simulations. It supports multiple force-fields and allows users to customize parameters, facilitating molecular dynamics and simulations.

This repository contains force field parameters and input files for conducting molecular dynamics simulations using GROMACS and Monte Carlo simulations using CASSANDRA. It is aimed at facilitating research in ionic liquids and includes relevant files for studying phase equilibria and thermodynamic properties.

PolymerAssembler is a Python tool that facilitates the quick construction of atomistic 3D polymer models using a probabilistic Markov model. It is particularly useful for molecular mechanics force field simulations and allows users to influence the degree of branching in polymers.

FFP4MOF is a Python library designed to calculate force field precursors for metal-organic frameworks (MOFs) using machine learning. It takes CIF files as input and outputs JSON files containing various calculated parameters, facilitating molecular simulations and property predictions.

MEAM-BO is an implementation of the Modified Embedded Atom Method with Bond Order in LAMMPS, designed to enhance molecular dynamics simulations by incorporating bond order calculations. This tool allows for more accurate modeling of materials by distinguishing different bond orders in various molecular structures.