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a python package for the interfacial analysis of molecular simulations

Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates

code for converting Gromacs molecular dynamics trajectories into inelastic neutron scattering spectra generated at the VISION instrument at ORNL.

reactive steps @ molecular dynamics

Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

Stochastic Reaction Model

Tutorial for new student to the group

This version will collect parameter from antechamber

with loop crosslinking algorithm v0.0.2

Generate the polymer crosslinking network starts from a mol2 file to a gro file

Construct substrates for molecular dynamics simulations.

Pore generator for molecular simulations.

The Molecular Simulation Pipeline simplifies molecular dynamics simulations with GROMACS and dockings with AutoDock Vina. Therefore it facilitates the communication to a computational cluster and p…

This is a simple python script to automate the molecular dynamics and minimisation protocols with gromacs. Current version can perform minimisations of protein-ligand complex only

This repository provide a automated method for Umbrella Sampling simulations to calculate binding energy between receptor and ligand.

Correlation computation package for gromacs

This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology file

2 days course to learn basic Linux terminal and GOMACS usage

Database of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Gromacs, NAMD, CHARMM, LAMMPS, TINKER, CNS/X-PLOR, Q, DESMOND, BO…

Processing code for analysing ouput from Gromacs using voro++

Code to implement the principle of maximum entropy with gromacs

script enabling topology editing for calculating system energies in gromacs

OPLS Forcefield for Gromacs for Polyfluorene (PF8, PF5, PF6)

Open source molecular dynamics analysis tools for GROMACS

Python package for molecular structure and Gromacs topology manipulation

GROMACS in-house post-analysis code

Perl scripts for polymer modeling using GROMACS

Utilities for GROMACS Molecular Dynamics Simulations