Using Avogadro on AI.Panther

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Avogadro is available through Open OnDemand for building, editing and viewing molecules.

To start it, go to ood.fit.edu, open Interactive Apps, and choose Avogadro. Set a GPU count of 1 on the form so the 3D view runs on the graphics hardware.

The first time you launch it, Avogadro offers to set up a Python environment for its input file generators. Answer yes. It takes a few seconds and needs no network access. Those generators build input files for ORCA and NWChem, both of which are installed on the cluster.

Avogadro is an editor rather than a solver, so the session is sized smaller than the other apps and is capped at 24 hours. Build your structure here, then submit the calculation itself as a batch job.

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Article ID: 24235
Created
Fri 11/13/26 9:35 AM
Modified
Fri 11/13/26 1:45 PM