schrodinger

General Information

The Schrodinger Suite is a licensed physics-based computational platform which integrates differentiated solutions for predictive modeling, data analytics, and collaboration to enable rapid exploration of chemical space.

To use Schrodinger on the cluster, you will need to load the appropriate module for the version you want to use. Schrodinger is a restricted license software, meaning it requires a license to use on the cluster. Contact [email protected] If you require assistance with how to obtain a license. And email [email protected] separately for inquiring about access to the software on HPC. The following example shows how to load the Schrodinger module (the$ is the prompt; do not type it). First, you have to load the RestrictedLicense preset. 

$ module load RestrictedLicense
$ module load schrodinger/2024-2

To use a specific version, check which versions are available with this module command.

$ module available schrodinger

Then load the version you want. Please see our page on Lmod for more information on loading modules.

Requesting access to Schrodinger

Contact [email protected] to request access to the Schrodinger software package. For licensing inquires contact [email protected]

Submitting Jobs with Schrodinger

Interactive Mode

If you require an interactive graphical interface, you can submit jobs through the Open OnDemand Desktop applications. Please refer to our Open OnDemand guide here. Once you have a desktop allocation, open a terminal window and execute the following commands. The last command will start the maestro window.

Batch Mode

When running schrodinger scripts on the cluster, especially for larger jobs, it’s recommended to submit them through SLURM or other job scheduling systems. Suppose you have a simulation program my_sim.sh. You can run this in batch mode by creating a SLURM script that looks like this (my_job.slurm):

#!/bin/bash
#SBATCH --job-name=my_maestro_job
#SBATCH --output=output.txt
#SBATCH --ntasks=1
#SBATCH --time=01:00:00
#SBATCH --mem=4G

# Load the RestricedLicense and schrodinger module
module load RestrictedLicense schrodinger

# Run your simulationb below
./my_sim.sh

Submit this script with the sbatch command:

$ sbatch my_job.slurm