About GROMACS

From Bootable Cluster CD

GROMACS (Groningen Machine for Chemical Simulations) is a molecular dynamics package. It is available freely under the GNU General Public License.

In addition, GROMACS also has a set of four simulations released to be used as benchmarks, called the GROMACS benchmarks. A description of the benchmarks may be found on the GROMACS website here.

GROMACS is not a part of the BCCD by default but it can easily be installed with the list-packages command. This is covered in more detail in the Running GROMACS tutorial.

Contents 1 Using GROMACS 1.1 grompp 1.2 Synchronizing 1.3 mdrun 2 GROMACS Files 2.1 .gro 2.2 .mdp 2.3 .top 3 More Information

Using GROMACS

Running a GROMACS simulation consists of three steps: running grompp, synchronizing the results over the computers to be used, and running mdrun. All of these are covered in more detail in the Running GROMACS tutorial.

grompp

Before running GROMACS, the GROMACS preprocesser (grompp) must first be run on the simulation and the number of processors must be specified. Within the folder containing the simulation, the following command must be run:

grompp -np 4 -shuffle -sort -v

• -np indicates the number of processors. In the above, four will be used.
• -shuffle distributes the loads equally amongst the processors.
• -sort indicates that atoms should be sorted by their coordinates, further helping parallelization.
• -v stands for verbose, meaning to output to the screen as it is running.

Synchronizing

First, all the computers running the BCCD on the same network must be "talking" to each other. This is accomplished by running the next three commands.

bccd-allowall
bccd-snarfhosts
bccd-checkem machines

Next, all the computers must have access to the grompp results. The following command creates a temporary folder that will exist on all the computers.

bccd-syncdir <path to the directory with your simulation> machines

mdrun

Finally, GROMACS is run with the mdrun command from within the temporary directory created in the synchronization step.

mpirun -np 4 -machinefile ~/machines /usr/local/bin/mdrun -v -c output.gro

• -np indicates the number of processes. This must be the same as specified to the grompp.
• -c specifies the name of the output file. This file should have an extension of .gro
• -v stands for verbose, meaning to output lots to the screen while running

GROMACS Files

With the GROMACS benchmarks installed through list-packages, the four simulations come with three files: conf.gro, grompp.mdp, topol.top.

.gro

conf.gro specifies the initial positions and velocities of the atoms. The output files produced when running the Running GROMACS tutorial will also be in this format.

The .gro files contain molecular structures in the Gromos87 format. A typical line might look like this:

  9ALA      N   87   3.492   2.996   1.618  0.1574  0.2410 -0.0154

• 9ALA is the name of the residue (group of atoms) that this atom belongs to.
• N is the kind of atom (nitrogen in this case).
• 87 is the unique number assigned to this atom.
• 3.492, 2.996, 1.618 are the x, y, and z positions of the atom.
• 0.1574, 0.2410, -0.0154 are the x, y, and z velocities of the atom.

For more information, see the gro page on the GROMACS online reference manual.

.mdp

grompp.mdp is a list of parameters to pass to grompp. For more information, see the mdp page on the GROMACS online reference manual.

.top

topol.top is a file that grompp uses to construct the topology of a simulation. For more information, see the top page on the GROMACS online reference manual.

More Information

For more information, please visit the GROMACS website at http://www.gromacs.org/. GROMACS also has an online reference manual available.