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Schrödinger Maestro is a versatile molecular modelling environment. It has modules for drug design and Materials Science. It can be used to build, edit, run and analyse chemical model systems.


Puhti: 2020.2, 2020.4, 2021.1, 2021.2, 2021.3, 2021.4, 2022.1, 2022.2

Mahti: 2021.4, 2022.1, 2022.2

Incompatibility issue with latest versions

Versions 2022.3 and later are incompatible with the RHEL8 operating system on Puhti and Mahti. If you intend to run jobs at CSC, don't upgrade your local installation beyond 2022.2! We're looking for a workaround.


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 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. These instructions to configure licensing require Haka authentication. Access to the license requires that your computer is in FUNET network, e.g. you're on the university or connected to it via VPN from home.

Standalone usage on Puhti


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 the heavy computations on Puhti. To do that you need to get a CSC accountCSC 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
  2. 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 on disk
  3. Copy them to Puhti
  4. Edit the script ( if needed
  5. Run the script on the Puhti command line to submit the jobs to the queuing system
  6. Copy the results back for analysis

The overall process is shown in the video below, and additional details and some diagnostics tips are explained in our Maestro power usage tutorial


Note, that 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:

"${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\"]" \
This is a bit complicated and it's best to write it out from the Maestro GUI as explained above. Please also have a look at the additional flags we recommend to use.

To run such a script in Puhti you first need to initialize Maestro (possibly edit it a bit) and run the script:

module load maestro

The following video tutorial walks you through it:

Maestro Standalone


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 due to lack of accelerated graphics. Also, no long/heavy tasks should be done on the login nodes. Please consult the policy on the computing overview page. If you need to run the GUI on Puhti, use the sinteractive command.


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

Desmond molecular dynamics runs very well on GPUs. We recommend watching the video above on how to accomplish this easily.

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 that warning, but consider any others you may see.


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: September 23, 2022