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Desmond/Maestro (for academic use only)


Desmond is a high-performance molecular dynamics (MD) code for biological systems developed by D. E. Shaw Research. Only GPUs are supported starting from the Desmond_Maestro_2019.1 release. For more information, visit the Desmond.


Access to Desmond/Maestro non-commercial version is granted to users who have registered to download Desmond. Licenses for the commercial use of Desmond are available from Schrödinger, LLC.
Access to other Schrödinger applications (ligprep, glide, prime, etc.) is restricted to subscribers of the HPRC-Laboratory for Molecular Simulation(LMS).

Desmond Registration

First, visit this page to complete registration. Acceptance of an End User License Agreement (EULA) containing the terms of registration is also required. Once accepted, several download links will be available.

Please send an email to stating that the user has registered and agreed to the terms and conditions to get access on HPRC clusters.

Loading the Desmond modules

Both Grace and Terra have Desmond modules available. To find available versions, use the following command:
On Grace:

[NetID]@grace ~]$ mla desmond

On Terra:

[NetID]@terra ~]$ ml spider desmond

To load a particular Desmond module:

[NetID]@grace/terra ~]$ ml Desmond/2021-1

Running Desmond in the Portal

It is suggested to run Maestro using VNC implemented under Interactive Apps in the Portal

You can request a CPU node (eg. 2 hours, 2 cores, 8GB memory, any node type)

Load the correct module. For example:
On Grace:

ml Desmond/2021-1

On Terra:

ml desmond/2021-1

Run Maestro:

A set of modules are preloaded to the portal to support the smooth running of graphical interface. ml purge should be used with caution. If the window decorations does not show up properly, please right click in the blank area and choose Fluxbox menu > Restart.

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