VMD-L Mailing List

From: Wei Chen (cwbluesky_at_gmail.com)
Date: Wed Dec 15 2010 - 14:55:24 CST

You can use catdcd to shrink your dcd files by selecting only protein atoms.

Wei

On Wed, Dec 15, 2010 at 11:46 AM, David Huggins <djh210_at_cam.ac.uk> wrote:
> 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