The Schrodinger molecular modeling software suite includes a number of popular programs focused on drug design and materials science but of general applicability, for example Glide, Jaguar, and MacroModel.  Maestro is the graphical user interface for the suite.  It 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.

Availability and Restrictions


The Schrodinger suite is available on Owens. The versions currently available at OSC are:

Version Owens
15 X
16 X
2018.3 X
2019.3 X
2020.1 X*
* Current default version

You can use  module spider schrodinger to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.


Schrodinger is available to all academic users.  

To use Schrodinger you will have to be added to the license server first.  Please contact OSC Help to be added. Please note that if you are a non-OSU user, we need to send your name, contact email, and affiliation information to Schrodinger in order to grant access. Currently, we have license for following features:


You need to use one of following software flags in order to use the particular feature of the software without license errors.

macromodel, glide, ligprep, qikprop, epik

You can add -L glide@osc:1 to your job script if you use GLIDE for example. When you use this software flag, then your job won't start until it secures available licenses. Please read the batch script examples below.  You can check your license usage via the license usage checking tool.

Publisher/Vendor/Repository and License Type

Schrodinger, LLC/ Commercial


Usage on Owens

To set up your environment for schrodinger load one of its modulefiles:

module load schrodinger/2019.3

Using schrodinger interactively requires an X11 connection. Typically one will launch the graphical user interface maestro.  This can be done with either software rendering:

maestro -SGL

or with hardware rendering:

module load vglrun
vglrun maestro

Note that hardware rendering requires a node with a GPU as well as the additional vglrun syntax above.  In principle hardware rendering is superior; however, in practice it can be laggier, and thus software rendering can yield a better experience.

Here is an example batch script that uses schrodinger non-interactively via the batch system:

# Example glide single node batch script.
#SBATCH --job-name=glidebatch
#SBATCH --time=1:00:00
#SBATCH --nodes=1 --ntasks-per-node=28
#SBATCH -L glide@osc:1

module load schrodinger
cp * $TMPDIR
host=`srun hostname|head -1`
nproc=`srun hostname|wc -l`
glide -WAIT -HOST ${host}:${nproc} -NJOBS 40
ls -l

The glide command passes control to the Schrodinger Job Control utility which processes the two options: The WAIT option forces the glide command to wait until all tasks of the command are completed. This is necessary for the batch jobs to run effectively. The HOST option specifies how tasks are distributed over processors.  In addition, the glide option NJOBS distributes the job into subjobs which can number more than the licenses or processors specified in the batch directives.

Determining the optimal amount of resources will probably require benchmarking.  See the Schrodinger Knowledge Base for advice, e.g., running glide in parallel and docking a large database.  Note also that OSC imposes a usage limit of 16 concurrent glide licenses per group. So while --ntasks-per-node=28 requests a whole Owens node, which may have significant performance benefits even if all processors are not used, it is not possible to have that many glide licenses.

Further Reading