GROMACS
Molecular Dynamics Simulation Software
 
 
 

GROMACS is an application package for performing large-scale molecular dynamics simulations. It is primarily designed for biochemical molecules like proteins and lipids but may also be used for simulating non-biological systems such as polymers.

GROMACS benefits include:

  • Fully automated topology builders for proteins, building blocks for 20 standard amino acid residues, 4 nucleotide and 4 deoxinucleotide resides, several sugars and lipids, and special groups like hemes and other small molecules
  • Fully parallelized for use on high-performance computers
  • Contains several state-of-the-art algorithms that make it possible to extend time steps in simulations significantly, thereby further enhancing performance without sacrificing accuracy or detail
  • Includes tools for trajectory analysis
  • User-friendly with topology and parameter files written in clear text format
 
Usage
GROMACS is available on the Bioinformatics cluster. To get an account on the cluster please see the Accounts page or contact Richard Casey below.
 
On the cluster, the GROMACS shell script

"gromacs_single.sh"

is available in the directory

"/common/gromacs"

You may copy this file to your home directory (or other locations) to run GROMACS. This shell script runs the single-CPU version of GROMACS (see below for parallel version).

Submit "gromacs_single.sh" to the batch queues on Bioinformatics cluster:

"qsub gromacs_single.sh"

Enter the command "qstat" to follow the progress of your batch job.

When the batch job is finished, results files will be sent to your home directory (or other directories as specified in the shell script).

GROMACS documentation (below) describes in detail how to use all the capabilities of the application. The gromacs_single.sh shell script can be modified accordingly to take advantage of these features.
 
Parallel Version
A fully parallelized version of GROMACS is available on the Bioinformatics cluster. It takes advantage of the cluster's 64-CPU architecture for high-performance molecular dynamics simulations.

On the cluster, the GROMACS shell script

"gromacs_parallel.sh"

is available in the directory

"/common/gromacs"

You may copy this file to your home directory (or other locations) to run GROMACS. This shell script runs the parallel version of GROMACS.

Submit "gromacs_parallel.sh" to the batch queues on Bioinformatics cluster:

"qsub gromacs_parallel.sh"

Enter the command "qstat" to follow the progress of your batch job.

When the batch job is finished, results files will be sent to your home directory (or other directories as specified in the shell script).

GROMACS documentation (below) describes in detail how to use all the capabilities of the application. The gromacs_parallel.sh shell script can be modified accordingly to take advantage of these features.
 
Documents
Documentation for GROMACS is available in the documents webpage.
 
GROMACS Website
For more information about GROMACS, visit the GROMACS website
 
Sample Molecular Dynamics Simulations
(mouse-over images to display video controls)
 
Dessicated Interferon alpha-2a
Solvated Interferon alpha-2a
Solvated Interferon alpha-2a
Interferon alpha-2a
 
Interferon alpha-2a ball-and-stick view
Interferon alpha-2a CPK view
 
Dessicated Interferon alpha-2a
Dessicated Interferon alpha-2a
 
 
For more information contact:
Richard Casey, PhD
Ph: 970-491-8568
Cell: 970-980-5975
Email: richard.casey@colostate.edu
 

© Copyright 2008, Colorado State University
Fort Collins, Colorado 80523
Maintained by Richard Casey