Schrodinger is a suite that is aimed to help the drug screening process (energy minimization, ligand-protein docking, building fragments, molecular dynamics, and so on). It is a widely-used application in the drug industries and in biomedical schools.
Version: Schrodinger-2010, Schrodinger-2011, Schrodinger-2012
License: Schrodinger's license is based on tokens which are reserved when you run jobs with multiple sub jobs. If you are planning to use it, please contact
to discuss about getting the permission, to talk about the restrictions or if you need to use more than 2 tokens.
To run Schrodinger jobs from the compute nodes, you are importing the graphic environment of Schrodinger to your local terminal. Since this requires a lot of connection bandwidth, please use wired campus connection for best usage.
To run serial Schrodinger Job in the cluster:
To run interactive maestro in the cluster:
If you need to do extensive molecular manipulation using maestro, you might want to use hpcviz.case.edu and NX access to run interactive maestro. The response time would be much faster than running maestro on the compute node. Since the hpcviz node is a common access node, please refrain from using this node for more than 1-2 hours.
NOTE: We recommend running Schrodinger job REMOTELY to avoid job being halted by broken X-connection.
To run Multiprocessor Schrodinger Job in the cluster:
Scenario: You are specifying 8 processors in maestro
You have to modify your qsub -I -X to request 8 processors.
qsub -l nodes=1:ppn=8 -X -I
In short, just change the value of ppn according to the number of processors you are specifying.
( Important Note: Keep in mind that you will also be checking out licenses equivalent to the number of requested processors so do not exceed your quota; you can monitor the licenses using the commands, /usr/local/matlab/matlabR2009b/etc/lmstat -a -c /usr/local/schrodinger/schrodinger-2010/license )
Run Schrodinger remotely from your local desktop:
Click on the appropriate links for descriptive instructions:
Some of the steps are outlined here too:
(! You will need to replace arc-login with hpcmaster in the above handouts)
Maestro Tutorial (Remote PC)
The desmond package is installed in hpctest (SLURM cluster).
This Desmond Guide can be helpful..