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Schrödinger Maestro is a versatile molecular modeling environment. It has modules for drug design and materials science. It can be used to build, edit, run and analyze chemical model systems.

Schrödinger Maestro provides access to the Desmond molecular dynamics engine, which runs very well on GPUs. We recommend watching the video below on how to set up and run Desmond MD simulations on Puhti easily.

See also the bottom of this page for links to further self-learning materials.


  • Puhti: 2022.3, 2022.4, 2023.1, 2023.2, 2023.3, 2023.4, 2024.1, 2024.2
  • Mahti: 2022.3, 2022.4, 2023.1, 2023.2, 2023.3, 2023.4, 2024.1, 2024.2

Pay attention to efficiency on Mahti

Note that Mahti is mostly suitable for running Desmond MD simulations on GPUs. Most other jobs do not scale to full nodes, so please use Puhti instead for these.

Module cleaning policy

A two-year cleaning cycle is applied on the Maestro modules on CSC supercomputers. Specifically, this means that module versions older than two years will be removed. This policy is enforced to free up disk space and encourage use of the latest versions which tend to be more performant and have less bugs.

Some notes about warnings

Maestro gives a warning for using a schrodinger.hosts file from your home directory. This is not an issue: that file cannot be made available in the installation directory, so please ignore the warning, but consider any others you may see.

Also, starting from module version maestro/2023.1 you might get warnings about missing graphics libraries. These warnings should be harmless. Nonetheless, if you would encounter unfamiliar issues using these Maestro versions, please contact CSC Service Desk.


Maestro is available for all academic users in Finland: staff and students, for academic purposes. Please consult the EULA for the exact definition. Using Maestro means that you accept the EULA linked to above. The Maestro license consists of floating licenses and tokens. If licenses run out, contact us via ServiceDesk.


It is recommended to download and install Maestro on your own computer, see below.

Local Installation

Maestro can be installed on a Linux, Mac or Windows computer. Download the appropriate files from the Schrödinger website. You don't need a license to download the software, although you need to register to the Schrödinger website, but you'll need to configure licensing before you can run it. See these instructions on how to configure licensing (requires Haka authentication). Access to the license requires that your computer is in the FUNET network, i.e. you're at the university or connected to it via VPN from home.

Standalone usage on Puhti

Please update your schrodinger.hosts file

The login nodes of Puhti were renamed following the RHEL8 upgrade in October 2022. Consequently, old schrodinger.hosts files referencing puhti-login1 will not work anymore! Please update your hosts file either manually by replacing all occurrences of login1 with login11, or by deleting your old schrodinger.hosts file and setting a new one by running the /appl/soft/chem/schrodinger/set-hosts-file.bash script.

Also, using public host addresses (ending with, e.g. in the hosts file might cause timeout issues, so these should be changed to internal ones, i.e. puhti-login11 (without

Puhti vs. Mahti

We mainly recommend using Puhti to run your Maestro jobs. If running on Mahti, you must ensure that your jobs are able to utilize full nodes (128 CPU cores). Preferably, run only Desmond MD simulations on GPUs because most other jobs do not scale. If in doubt, contact us.

It is possible to run heavier computations on Puhti. Here, a brief overview is given. Additional details and some diagnostics tips are explained in our Maestro power usage tutorial. See also the video below.

First, you need to get a CSC account and apply for access to Puhti. Before you start the actual workflow below, you need to set up your Maestro environment on Puhti.

These first four steps you only need to do once:

  1. SSH to Puhti
    • ssh <your username>
  2. Initialize Maestro with module load maestro
    • Make sure you use the same version as on your local computer
  3. An error may appear on your screen. If it asks you to run a script to generate the hosts file, run it (copy paste it to the command line)
    • Now you have your own schrodinger.hosts file in your $HOME directory
  4. Copy the HOST descriptions from the schrodinger.hosts file on Puhti to your local hosts file on your computer
    • Copy everything starting from name: test and paste it at the end of your local schrodinger.hosts file
    • This step may need administrator privileges

For actual simulations we recommend using Puhti as follows:

  1. Set up your simulations on your local computer
  2. Write the GUI-generated input files to disk
  3. Copy them to Puhti with e.g. scp or through the Puhti web interface
  4. If needed, edit the submission script (
  5. Run the script on the Puhti command line to submit the jobs to the queuing system
  6. Copy the results back for analysis


Maestro jobs are not run via batch scripts like most other applications at CSC, but via Schrödinger binaries using options.

For example, a Desmond workflow could be run with the script:

"${SCHRODINGER}/utilities/multisim" -JOBNAME 2hhb_test -HOST gputest  \
-maxjob 1 -cpu 1 -m 2hhb_test.msj -c 2hhb_test.cfg -description "Molecular Dynamics" \
2hhb_test.cms -mode umbrella -set stage[1]["-gpu"] \
-o 2hhb_test-out.cms -lic "DESMOND_GPGPU:16 -set "stage[1]["\-LOCAL\"]" \

The scripts tend to be somewhat complicated, so it's best to write them out from the Maestro GUI as explained above. Please also have a look at the additional flags we recommend to use.

To submit such a script in Puhti, you need to first load Maestro and then run the script

module load maestro

Maestro GUI

We do not recommend running the Maestro GUI remotely on Puhti. It can be done via the Puhti web interface remote desktop, but the performance may be somewhat slow and submitted jobs may end up fizzled. Also, no long/heavy tasks should be done on the login nodes. Please consult the Usage policy page for more details.

Note for Windows users

Windows users may need to edit the script created by the GUI a little. Replace the backslashes \ with / in the path to the Maestro binary (right after $SCHRODINGER in the script).

Video: How to run a Desmond simulation on Puhti

The following tutorial video walks you through the process:

Maestro Standalone


Please cite the Maestro modules in all published work as described in the Module manuals. Jaguar, for example, should be acknowledged with:

Jaguar, version 7.6, Schrödinger, LLC, New York, NY, 2009.

More information

Last update: May 6, 2024