From: Axel Kohlmeyer (
Date: Thu Dec 16 2010 - 04:29:53 CST

On Wed, Dec 15, 2010 at 2:46 PM, David Huggins <> 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?

it is not a problem of NAMD, but the file format. dcd files require
that in each step the number of atoms is the same, and also it is
assumed that the atom identity is the same, since the dcd file only
stores lists of coordinates without any indexing.

hence per-region dcd files are not possible.


> Thanks very much,
> Dave

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.