Cluster:GROMACS Web Interface

Masa's GROMACS web interface is now running on c0 at the following URL:

http://c0.cluster.earlham.edu/GROMACS.

Usage Notes

• You need a molecule in PDB format which you can get from RCSB PDB.
• Many molecules need supplementary files that are not included with GROMACS. The web interface seems to have no way to add these supplementary files.
• The interface is not extremely robust at this point. Be prepared to run your MD more than once.

Environmental Notes

• The tmp directory inside the web interface's directory structure needs to be rwx to the php user (apache with default group of nogroup in the case of c0). Right now, the directory is owned by root.software with 777 permissions but should probably be changed to something more secure soon.

Source Changes

• After line 66 in gromacs.php the environment of the created csh scripts need to have the PATH to the GROMACS binarues and GMXLIB both need to be set. In the case of c0, the changes look like the following:

 $string4 = $string4 . "setenv PATH /cluster/cairo/software/gromacs-3.2.1-Optimal/powerpc-unknown-linux-gnu/bin/\n";
 $string4 = $string4 . "setenv GMXLIB /cluster/cairo/software/gromacs-3.2.1-Optimal/share/top\n";