JUSTUS2/Software/Schrodinger: Difference between revisions

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'''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.
'''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.


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== Versions and Availability ==
= Versions and Availability =
Schrödinger, especially Maestro, is available after registering for academical use for no charge. Downloadable here: [https://www.schroedinger.com/downloadcenter/ Download Center]<br>
A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the
Your request will be verified and after that you can download Maestro for academical use. That will take about 48 hours.

<big>[https://cis-hpc.uni-konstanz.de Cluster Information System CIS]</big>
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|url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/chem/schrodinger
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On the command line interface of any bwHPC cluster you'll get a list of available versions by using
the command
module avail chem/schrodinger

The module is called ''''schrodinger'''' and '''not''' 'schoedinger' or 'schrödinger'!
<br>
-->
= 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:
== Prerequirements ==


# X11 forwarding via <code>ssh -X username@justus.uni-ulm.de</code> from a unix machine (simple but very slow, only barely suitable from university network)
=== Requesting the License Key ===
# a remote desktop via VNC.
After installing Maestro you need a license key which you can request from the „Competence Center for Bioinformatics“. Please contact


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.
==== Set environment variable for the license server ====
When you got the licence server information, set it as an environment variable, editing $LICENSE_SERVER$ in the following command.
<pre>export LM_LICENSE_FILE=$LICENSE_SERVER$</pre>


You can connect to the visualization hosts
On a Mac system you should additionally execute following tasks
<pre>
<pre>sudo vi /etc/launchd.conf</pre>
justus2-vis01.rz.uni-ulm.de
justus2-vis02.rz.uni-ulm.de
</pre>
of the system to access the graphical interface "maestro" using a vnc viewer.


Please follow the documentation on our page on
Insert: <pre>setenv LM_LICENSE_FILE $license_server$</pre> and save the file.


&nbsp;&nbsp;&nbsp;&rarr; [[JUSTUS2/Visualization|Visualization using VNC]]
Execute following command and start Maestro from Sportlight:
<pre>launchctl setenv LM_LICENSE_FILE $LICENSE_FILE$</pre>


⚫
== Running ==
=== Prepare job release on the cluster ===
If you are on one of the vis servers inside VNC:


<code>vglrun maestro -NOSGL</code>
==== Edit schrodiger.hosts ====


on normal login hosts inside VNC without hardware accelerations
under construction


<code>maestro -SGL</code>
⚫
== Usage ==


To start maestro in the mode for the other suites:
=== Copy your public key ===
Maestro needs a passwordless login for submitting jobs on the cluster.
Login to the cluster and copy your public key of your host system from <tt>.ssh/id_rsa.pub</tt> into <tt>.ssh/authorized_keys</tt> file on the cluster.


* <code>vglrun maestro -profile BioLuminate &</code>
=== Using Maestro with the offered example ===
First start Maestro and choose the following menu items:
[[File:usage01.jpg]]


* <code>vglrun maestro -profile Elements & </code>
Then load the molecularDynamicsExample.cms from your filesystem:
[[File:usage02.jpg]]


* <code>vglrun maestro -profile MaterialsScience &</code>
Choose your desired host and click ""Run"".
[[File:usage03.jpg]]


=== Monitoring you job ===
Maestro offers an job monitoring interface, which you can start in the left corner of the molecule window.
[[File:monitor01.jpg]]
Furthermore you are able to manipulate you job on the cluster.


== Examples ==
== Submitting Jobs ==
You can submit jobs from within the Schrödinger GUI Maestro.
Download: molecularDynamicsExample.cms
Make sure to only run calculations on localhost directly for short minimalizations and submit to the compute nodes for any longer runs.

Latest revision as of 13:03, 10 December 2025

The main documentation is available on the cluster via module help chem/schrodinger. Most software modules for applications provide working example batch scripts.


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:

  1. X11 forwarding via ssh -X username@justus.uni-ulm.de from a unix machine (simple but very slow, only barely suitable from university network)
  2. 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

   → Visualization using VNC

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.

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