Co-ordination & Harmonisation of Advanced e-Infrastructuresfor Research and Education Data Sharing

Research Infrastructures – Proposal n. 306819

GROMACs

GROningen MAchine for Chemical Simulations

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

Overview

Overview

http://www.gromacs.org

It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the non-bonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

Introduction

Tools

GROMACs contains several tools and commands that allow a diverse range of biological functions to be performed. The tools we most used were:

• Mdrun• Mpimdrun

Tools

Mdrun is the main command of the AutoDock portfolio. It begins the basic molecular dynamics calculus after all the other parameters have been set.

mdrun

This command executes the same commands found in mdrun, but it’s the process of execution which is different. This command executes molecular dynamic functions as an MPI application, thus distributing the number of steps between several computers.

mpimdrun

The distribution of functions and use of checkpoints reduces the time needed to finish a single simulation, and allows for several simulations to run in parallel.

mpimdrun

Resources needed

A single GROMACs simulation can take between 16-48 hours, depending on the initial conditions, and several running at the same time can take more.

Resources taken on the computer are defined, but more cores mean faster simulations, which is why more infrastructure is much desired.

Use on the GISELA Infrastructure

We consider that incorporating GROMACs into the GISELA infrastructure will allow several biologists and chemical engineers to run molecular dynamics simulations, thus helping them hone their results before conducting lab tests, and reducing costs, without the need of having the computational resources on campus.

The work towards GISELA

People at the Universidad de Los Andes have worked with the chemical engineering department to run several molecular dynamics simulations.

Thanks to the works done together with the INFN of Catania a first portlet using GROMACS have seen the light!

First Experience

Shool in the 2012

Integration in CHAIN-REDS

The input files

http://manual.gromacs.org/current/online/tpr.html

Right now the installed version on the e-Infrastructure is the 4.5.3 on SL5

Project partner need a more updated version Installation of version 4.5.6 is under test on SL6 Once the installation is tested, update the

portlet on the portal.

Future Works

Make the application use mpirun, find a use case

Add other tools apart from mdrun Having back the input file readable

Suggested improvement

Co-ordination & Harmonisation of Advanced e-Infrastructuresfor Research and Education Data Sharing

Research Infrastructures – Proposal n. 306819

Questions ?