How-to

The actual job is best prepared with the Maestro GUI either on your own local machine or in Hippu. It can also be done in Vuori compute node (via salloc -n 1 srun maestro), but the response to interactive use is better in the other options. The NoMachine remote desktop is recommended for remote Maestro usage.

After the system has been set up (Applications -> Desmond -> System Builder; and e.g. Applications -> Desmond -> Molecular Dynamics) write the files to disk by choosing "write" from the "Molecular Dynamics" window. This will result in two files with extensions .cms and .cfg. Copy these to Vuori $WRKDIR and load the Desmond environment and run the job:

module load desmond/2009.2
desmond -HOST parallel -PROCS 8 -in butane_md.cms -c butane_md.cfg

For MORE CSC specific information, Please have a look at the Maestro page for more options. and

You can download the Free for Academic use -Desmond directly from D.E. Shaw research for local installation.

You can try the above submission script with these input files: desmond-test.tar.gz  Have a look at the README file, too.

wget http://www.csc.fi/english/research/sciences/chemistry/maestro_files/desmond-test.tar.gz
gunzip desmond-test.tar.gz
tar xf desmond-test.tar
cd des-test
desmond -HOST murska-para-2days -PROCS 8 -in butane_md.cms -c butane_md.cfg