JUSTUS2/Software/Schrodinger
|
The main documentation is available on the cluster via |
| Schrödinger | |
|---|---|
| module load | chem/schrodinger |
| Availability | BwForCluster_Chemistry |
| License | commercial |
| Citing | 5. See Schrodinger manual |
| Links | Homepage | Documentation |
| Graphical Interface | Yes, Maestro, Desmond |
Description
Schrödinger is a collection of software chemical or biochemical use. It offers various tools, like Maestro, that acts like an interface to all other schrödinger software and it is supposed to be used for material science, to investigate the structure, the reactivity and properties of chemical systems. Maestro is part of the Materials science suite.
Availability
Schrödinger is available on the HPC cluster Justus2 to users of the system for no charge.
Remote Visualization
As Schrödingers "Maestro", the main interface of the Schrodinger Suite haas a graphical you will need to use some kind of remote desktop to connect to Justus2.
There are two supported ways:
- X11 forwarding via
ssh -X username@justus.uni-ulm.defrom a unix machine (simple but very slow, only barely suitable from university network) - a remote desktop via VNC.
For the second option, we have special visualization hosts that have graphics cards to enable you to view simulation cells with thousands of water molecules and your molecule smoothly.
You can connect to the visualization hosts
justus2-vis01.rz.uni-ulm.de justus2-vis02.rz.uni-ulm.de
of the system to access the graphical interface "maestro" using a vnc viewer.
Please follow the documentation on our page on
Running
If you are on one of the vis servers inside VNC:
vglrun maestro -NOSGL
on normal login hosts inside VNC without hardware accelerations
maestro -SGL
To start maestro in the mode for the other suites:
vglrun maestro -profile BioLuminate &
vglrun maestro -profile Elements &
vglrun maestro -profile MaterialsScience &
Submitting Jobs
You can submit jobs from within the Schrödinger GUI Maestro. Make sure to only run calculations on localhost directly for short minimalizations and submit to the compute nodes for any longer runs.