VMD-L Mailing List

From: David Huggins (djh210_at_cam.ac.uk)
Date: Wed Dec 15 2010 - 13:46:16 CST

Dear All,

I am running long NAMD simulations on a solvated protein and producing large
output DCDs.

Is there a way to only save a selection of atoms from the trajectory to the
DCD, to reduce its size? I am only interested in one region of the protein
but I'd like to use PBC and PME. Can NAMD cope with different numbers of
waters in each snapshot?

Thanks very much,

Dave