Fast estimation of ion-pairing for screening electrolytes

Basic tutorial for running and analyzing a Gromacs MD simulation of AdK

A molecular dynamics approach to study the permeation of nanoparticles through lipid bilayer

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

🔬 Gromacs yordamida molekular modellashtirish

singularity definitions of GROMACS

A singularity container demonstrating multi node MPI via SSH wrapper

Script developed to run the commands of the "Lysozyme in Water" tutorial in gromacs in different force fields at once

Script developed to run the commands of the "Lysozyme in Water" tutorial in gromacs.

A Molecular Dynamics simulation project of pyrazinamidase studying its influence in antibiotic resistance of pyrazinamide. The TIP3P water model as implemented in CHARMM (MacKerell) specifies a 3-site rigid water molecule with charges and Lennard-Jones parameters assigned to each of the 3 atoms. In GROMACS the fix shake command can be used to ho…

Transfer Li ions from cathode to anode in MD simulations

Conda package of gromacs 5.1.2 intended for testing purposes.

Simulate interactions between two fully-charged PAA chains with varying amounts of CaCl2 added

Bash shell scripts that process GROMACS files for automating a series of molecular-dynamics (MD) simulations on NERSC supercomputer.

A collection of scripts and software to assist with biomolecular simulation in our laboratory

GROMACS implementation of PVDF/CNT FF. PVDF from Sahihi et al. , J. Phys. Chem. C 2021 125 (39), 21635-21644, DOI: 10.1021/acs.jpcc.1c05894. CNT from OPLS-AA.

Tutorials workstation for MD.

Automatisasi simulasi MD menggunakan gromacs untuk multi kompleks protein-ligand dimana setiap kompleks terdiri dari resepetor dan 1 ligand.

A gromacs tutorial for creating a gromos54A7 simulation system of a protein in a simple membrane

Shell script to prepare protein PDBs for GROMACS molecular dynamics simulations, with SLURM script included to run md with hpc