This document discusses GROMACS, a software package for molecular dynamics simulations. GROMACS can simulate hundreds to millions of particles and is primarily used for biochemical molecules like proteins, lipids and nucleic acids. It contains tools like mdrun for basic molecular dynamics calculations and mpimdrun, which executes mdrun in parallel across multiple computers. Running GROMACS simulations can take 16-48 hours depending on the system, and using more computational cores allows faster simulations. The document proposes making GROMACS available on the GISELA e-infrastructure to allow researchers to perform molecular dynamics simulations without needing local computational resources.

1. Co-ordination & Harmonisation of Advanced e-Infrastructures
for Research and Education Data Sharing
Research Infrastructures – Proposal n. 306819
GROMACs
GROningen MAchine for Chemical Simulations

2. 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

3. Overview
http://www.gromacs.org

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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.

10. 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

11. 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

12. Shool in the 2012

13. Integration in CHAIN-REDS

14. The input files
http://manual.gromacs.org/current/online/tpr.html

15.  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

16.  Make the application use mpirun, find a use case
 Add other tools apart from mdrun
 Having back the input file readable
Suggested improvement

17. Co-ordination & Harmonisation of Advanced e-Infrastructures
for Research and Education Data Sharing
Research Infrastructures – Proposal n. 306819
Questions ?