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Convert gromacs input files to metalwalls format
MW-Gui is a builder and file preparator for simulation with Metalwalls software : a molecular dynamics package to perform constant potential simulations
BLADE (Boride Learning and Design Engine) is a high-throughput framework for screening oxidation-relevant properties of high-entropy diborides using special quasirandom structures (SQS), first-prin…
python scripts for setting up proton transfer QM/MM simulations with GROMACS and PLUMED, selection of initial frames, collective variable definitions, etc.
Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis
Multiple walker supervised molecular dynamics is now scalable and can run with NAMD, GROMACS and ACEMD.
A python GROMACS interface for MD simulations of organic molecular crystals
Molfileplugin for VMD that lets me read in GROMACS tpr files
ion permeation event counter and analyser for GROMACS trajectories
This code lets its users get different outputs related to cluster analysis from a GROMACS simulation trajectory for multichain systems. It is slightly different from the traditional cluster analysi…
Python tools to compute interchain and intrachain contacts from GROMACS trajectories using a PLUMED-style switching function. Supports PBC, chain-wise analysis, residue exclusion, and generates tim…
LiNaK is a lightweight Python toolkit for molecular dynamics trajectory analysis.
Automated DFT screening of Metal-Organic Frameworks (MOFs) for multi-ion anode material properties using CP2K.
This code is a driver (Fortran90) that enables path integrals simulations in conjunction with atomistic molecular dynamics simulation software (specifically CP2K). The code is general and can be us…
[https://bin-cao.github.io/PyWPEM] AI-Driven Structure Refinement of X-ray Diffraction
A workflow for training MACE machine learning potentials using CP2K and LAMMPS
The program allows you to create regular structure supercell from cif file with partial occupancy and/or substitutions.
Python scripts to convert CGenFF stream files to GROMACS format
PaCS-Toolkit: Optimized software utilities for PaCS-MD and following analysis
Automated framework for QM-region preparation, xTB quantum calculations, and advanced statistical analysis of GROMACS MD trajectories.
This repository provides an automated python code for generating a layer of NGS-1 chromophores on SiO2 (001) surface to simulate classical MD simulations using GROMACS. Slabsize and occupancies can…
Collection of shallow wrappers around popular Neural Network potentials for use with the NNPot interface in the GROMACS molecular simulation toolkit.
A tutorial on free energy simulations using the GROMACS software
Perform polymerization and crosslinking in MARTINI coarse-grained forcefield using GROMACS MD package
Shell and python framework for automated molecular dynamics simulations using GROMACS, with optional SAXS-based trajectory analysis.
A python package for performing GROMACS simulation ensembles
OpenFFGen is a Python-based pipeline that converts .pdb molecular structures into simulation-ready input files for LAMMPS and GROMACS. It leverages the OpenFF to generate consistent and reproducibl…