GROMACS-Run-Files

This repository contains run files for animations uploaded to https://space.bilibili.com/402206352/video

Common Files

• run.sh is a bash script for conducting the full simulation. It builds the initial configuration and the simulation box, do energy minimization and then run NVT/NPT simulations. You might want to modify .mdp files before running this script.
• xvgplot.ipynb is a python script for plotting .edr files generated during simulation.

NOTE that you may need to download the force field files in the top/ directory and include them correctly in topol.top.

Software and Online Services used in simulations

GROMACS is a free and open-source software suite for high-performance molecular dynamics and output analysis.

https://www.gromacs.org/

Packmol is a free software for creating an initial point for molecular dynamics simulations by packing molecules in defined regions of space.

https://m3g.github.io/packmol/

ATB is a free online service that provides classical molecular force fields for novel compounds. It can automatically generate topology files for small molecules. It also provides a database of existing molecules.

http://atb.uq.edu.au/index.py

TPPmktop is a free online service that automatically generates topology files for OPLS/AA force field.

http://erg.biophys.msu.ru/erg/tpp/