Schrödinger

Introduction#

The Schrödinger suite is a commercial and licensed software used to simulate and model molecular behavior at the atomic level. The Schrödinger software tools include molecular dynamics simulations, quantum mechanics calculations, virtual screening and visualization tools.

Schrödinger on Sherlock#

Licensing#

Stanford Libraries have purchased a site license for the Schrödinger suite. Please contact Stanford Libraries at sciencelibrary@stanford.edu and CC srcc-support@stanford.edu if you would like to access Schrödinger on Sherlock: after we receive confirmation, your PI group will be granted access on Sherlock.

Using Schrödinger#

You can use Schrödinger software after having loaded the corresponding software module with the module command. To load the current default version:

module load chemistry schrodinger

To see all the available versions, you can use the module spider command:

$ module spider schrodinger

Once loaded, the $SCHRODINGER environment variable is automatically set to allow all Schrödinger commands to run. For example, to run the jaguar command:

$ jaguar run -WAIT H20.in

To call the basic Schrödinger run command, just enter:

$ run

or glide:

$ glide
usage: glide_startup.py [options] <input_file>
glide_startup.py: error: the following arguments are required: input_file

Maestro GUI#

OnDemand shell sessions

Opening an X11/GUI session will not work in a Sherlock OnDemand terminal session. You will need to use the method mentioned below, i.e. a standard terminal session with an X11 client.

To launch the Maestro GUI, once you have loaded the Schrödinger module, simply run:

$ maestro

You'll need to enable X11 forwarding in your initial connection to Sherlock, and request it as well for your job allocation.

Here are some example commands you can run:

# on your local machine
$ ssh -X login.sherlock.stanford.edu

# then from a Sherlock login node
$ sh_dev -m 16GB

# and finally on the allocated compute node:
$ ml load chemistry schrodinger
$ maestro

This will launch Maestro on a compute node and display its graphical user interface on your local machine's display.

GUI performance

Please note that running graphical user interfaces (GUIs) over the network via X11 over SSH may not necessarily yield the best performance. Graphical analysis is often best done on a local machine, while intensive, batch scheduled computations are carried over on the cluster.

For more information about X11 forwarding, you can refer to this page.

Examples#

batch job submission#

Here's an example batch script, requesting 1 CPU, for 10 minutes on the normal partition, that can be saved as water.sbatch:

#!/usr/bin/bash
#SBATCH -o water.%j.out
#SBATCH -e water.%j.err
#SBATCH -n 1
#SBATCH -t 10:00
#SBATCH -p normal

# Load required modules
module load chemistry schrodinger

# Run Schrödinger, -WAIT is often required
jaguar run -WAIT H20.in

Save this input file as H2O.in:

&gen
&
&echo
&
&zmat
O       0.0000000000000   0.0000000000000  -0.1135016000000
H1      0.0000000000000   0.7531080000000   0.4540064000000
H2      0.0000000000000  -0.7531080000000   0.4540064000000
&

And you can submit the batch script with:

$ sbatch water.sbatch

After execution, you should find a H20.out output file in the current directory, as well as a log file (H20.log). If you don't, you can check for errors in the job output and error files: water.<jobid>.{out,err}.