Encore.cluster very slow

MDAnalysis / mdaencore

Ensemble overlap comparison software for molecular data.

http://www.mdanalysis.org/mdaencore/

GNU General Public License v2.0

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Encore.cluster very slow #71

Open khoroshyy opened 1 week ago

khoroshyy commented 1 week ago

HI. I am trying to cluster ligand conformations using encore cluster. cluster_collection = encore.cluster(u, select="resnum 10834 and not name H*", ncores=10) But it is extremely slow, is there a way to speed it up. I have 10000 frames of 70 atoms. Thanks. Petro.