MCSR

Before you begin, please copy the Gromacs examples to your home directory and enter the tutor directory with the following commands:

cd mkdir gromacs cp -r /usr/local/appl/gromacs-3.3.1/share/gromacs/tutor/ gromacs/ cd gromacs/tutor

Now you can begin running the examples:

Enter the directory of the example you want to run *.
This tutorial will use the "water" example:

cd water
Use grompp to create input files for the number of processors you will run your job on. This example will use 4 processors. We must use grompp's -np option to generate input files for multiple processor (parallel) simulations. A 4-processor job will require 4 input sets, so here we use -np 4:

grompp -np 4
Now that we are ready to run the simulation, create a PBS script for your job and submit it. See PBS at MCSR.

Your script must invoke the parallel mdrun executable (called mdrun_mpi) using mpirun. This executable is found in /usr/local/appl/gromacs-3.3.1/bin (this is used below in our PBS script).

Because mdrun_mpi reads input from the current directory, we must enter the working directory of the current simulation, within our PBS script. The following example PBS script will run the "water" example, located in /my/home/gromacs/tutor/water, on 4 processors.

Note that you must specify the number of processors in three places.:

#PBS -S /bin/bash #PBS -l ncpus=4 #PBS -l mem=500MB #PBS -l cput=10:00:00 #PBS -N gmx_water_4p cd /my/home/gromacs/tutor/water mpirun 4 /usr/local/appl/gromacs-3.3.1/bin/mdrun_mpi -np 4
This completes the introduction to running basic Gromacs simulations on Redwood. Most of the examples can be run in serial fashion by simply running grompp ** and then mdrun ** from the example's respective directory. This may help in determining your parallel performance increase.

In study, it has been determined that the water example runs best on 4 processors, while the mixed example runs best on 2, and the nmr1/nmr2 examples see very little parallel performance increase due to their low number of iterations. Your results may vary.

To see more in-depth tutorials using these same examples, and information about analyzing the resulting data and performing more complex simulations, see:
- Getting Sgarted
- gmxdemo
- water
- methanol
- mixed

You may need to append the Gromacs binary directory to your PATH environment variable to use some of these tutorials. See note ** below for more information.

* gmxdemo is not wholly interactive and does not follow the instructions outlined here. However, it is a good starting place for new Gromacs users. Additionally, the speptide demo requires the user to do some additional steps, which are not outlined here. Please see this tutorial for running the speptide example.

** You may need to append the Gromacs binary directory,

/usr/local/appl/gromacs-3.3.1/bin

to your PATH environment variable to run grompp, mdrun, and other Gromacs executables.
See Managing your Environment for more help with changing your PATH environment variable.