Extract Trajectory Without Water and Ions

Acellera / htmd

HTMD: Programming Environment for Molecular Discovery

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Extract Trajectory Without Water and Ions #1087

Closed vas2201 closed 5 months ago

vas2201 commented 5 months ago

Hi,

I have completed the production run and need to extract the trajectory excluding water and ions. Could you please assist by providing the script for this task?

Thank you for your help.

Best regards, Vas

stefdoerr commented 5 months ago

from moleculekit.molecule import Molecule

mol = Molecule("./structure.prmtop")
mol.read("./output.xtc")
mol.filter("not water and not ion")
mol.write("./output_filtered.xtc")