Andy Watkins

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icon company Prescient Design icon location United States icon location PhD NYU (Arora); postdoc Stanford (Das); now Director of Structural and Computational Biology at Prescient Design (Genentech)

Results 4 comments of Andy Watkins

Gradual slow down when running dynamics on Perlmutter A100 GPUs

Could your Torch module be accumulating state in a way that increases GPU memory usage or consumption or demands CPU offloading?

error while trying to predict the structure

You may want to format your fasta like in the example -- with separately indicated H and L chains.

Integrate with RiboDraw

Another way to approach this -- I don't know which is easier? -- is to make RiboDraw output a data format that meets the R2DT spec for a template. Since...

Integrate with RiboDraw

Yeah, routing through this sort of XML format is probably reasonable. And it's easy enough to encode edge, edge, orientation as `[WHS][WHS][CT]` (for example, if you're in the mood for...