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Schrödinger Software

Table of contents

General Information:

Schrodinger Software provide accurate, reliable, and high performance computational technology to solve real-world problems in life science research. It can be used to build, edit, run and analyse molecules. For more details please consult the schrodinger Home page. 

Please note that the number of licenses for Schrodinger applications /or modules  is limited to 50 floating licenses at LRZ.

Schrodinger products

The Schrödinger-Suite of applications have a graphical user interface called Maestro. Using the Maestro you can prepare your structure for refinement.

Click "Applications" and select the respective program. The following products are available: CombiClide, ConfGen, Core Hopping, Desmond, Epik, Glide, Glide, Impact, Jaguar ( high-performance ab initio package), Liaison, LigPrep, MacroModel, MCPRO+, Phase, Prime, PrimeX, QikProp, QSite, Semi-Empirical, SiteMap, and Strike. 

Jaguar: is an ab initio quantum chemistry software package developed by Schrodinger. It is rather fast, and has an extensive list of features. Some simple tasks (HF and DFT optimizations and closed-shell MP2 energies) can be performed in parallel. Jaguar can be used using a graphical user interface (see below) or  by command line.

MacroModel: is a molecular modeling software package allows the user to construct and graphically manipulate both simple and complex chemical structures, to apply molecular mechanics and dynamics techniques to evaluate the energies and geometries of molecules in vacuo or in solution, and to display and examine graphically the results of the modeling calculations.

Usage at LRZ

The module package  controls access to software. To use Schrödinger-Suite  please load the module environment appropriate  first after login to the system via:

% module load schrodinger

You can use the application as command line via:

% jaguar run -PROCS XXX -HOST YYY mol.in

For more iformation type:   

ls -C  $SCHRODINGER_DOC

To start Maestro graphical user interface , simply type:

% maestro -SGL

Else you can use the applications as command line via:

jaguar run -PROCS XXX -HOST YYY your-input.file

 or with the remote visaalisation server using rvrun, for futher information please refer here.

maestro

maestro2

Job submission to Linux-Cluster (SLURM) and SuperMUC (LoadLeveler) systems at LRZ and job monitoring is administrated using Maestro. It is necessary that you run maestro on the corresponding platform in order to submit/run your jobs there. Therefore, e.g. first login to the cluster and MPP 

  ssh -X lxa1
and execute 
maestro -SGL
then you are able to select the host MPP to submit your job.

Note further that with submission to the queue your job typically does not start immediately. To check the status of your job, use 

squeue -u userID (SLURM)
or 
llq -u userID (LoadLeveler)
depending on your platform.

Be aware that "localhost" resources are limited and should not be overused since you share the cores with all other users..

Once the job starts running you will see 2 files: mol.log with essential calculation output, and mol.out with complete calculation output.

Please note: Maestro is also available on desmond module (for molecular modelling application Desmond), after executing: 

module load desmond

Manuals/Documentation

  •   The Maestro Installation provides manuals in html and pdf format. They are accessible from the Maestro interface page at "help" or can be found from the environment variable:    
    •         
    ls -C  $SCHRODINGER_DOC
  •   For futher information please refer to the Schrödinger Home Page.

Support

If you have any questions or problems with Schrödinger installed at LRZ platforms, please don't hesitate to contact LRZ HPC support staff .