Re: how to remove translational and rotational motion from dcd file

From: Neelanjana Sengupta (
Date: Thu Nov 09 2006 - 20:04:56 CST

After you do all your manipulations, do the foll:

animate write dcd newTraj.dcd beg $first end $last waitfor all sel $all $sys

have $last and $first correspond to your first and last frame, $all is a
selection for the entire system, and you designate $sys when specifying your
set sys [mol new myPSF.psf]

Hope this helps.

On 11/9/06, Dhiraj Srivastava <> wrote:
> Hi all
> I want to get coordinates from DCD file but before that i want to
> remove contribution from rotational and translational motion to the change
> in coordinates. also i want to remove coordinates of water molecule from dcd
> file. i know that matdcd can transfer coordinates from dcd file to matlab in
> matrix form thats what i need. i also know that i can remove contribution
> from rotational and translational motion to dcd file by aligning all other
> frame to reference frame. but after alignment, how can i write dcd file? is
> there any command to write dcd file from loaded trajectories in the vmd?
> thanks for help.
> --
> Dhiraj Kumar Srivastava
> Department of Chemistry
> University of Missouri-Columbia
> MO, 65211

Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
Phone: 1-949-824 9921

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:09 CST