From: Axel Kohlmeyer (
Date: Mon Apr 16 2007 - 19:46:08 CDT

On Mon, 16 Apr 2007, Philipp Schoen1 wrote:

hi philipp!

PS> Dear Users
PS> I want to grid my computational domain. What files do I need to do so?
PS> Currently I am loadng the trajectory dcd plus the velocity dcd. From the

hmmm.. usually you have to hack the dcd reader to accept velocity dcds.
are you sure that those were really loaded? VMD doesn't care about
velocities. the best way of handling this is usually to load the
corresponding .psf file into two molecules and then load the coordinates
into one and the velocities into the other.

PS> first one I want to get the atoms belonging to a certain box. From the last
PS> one I want to calculate the temperature. Is it possible by using these
PS> files? How can I load the velocity values for certain atoms belonging to a
PS> predefined sub-domain?

if you have those two 'molecules' + 'trajectories' as suggested before,
you can create a selection in the first one using a selection text
like '5 <= x and x < 10 and 5 <=y and y < 10 and 5 <= z and z < 10'
to select atoms in a given box and then use the subcommand 'list'
on the generated selection function to extract the atom indices and
then create a selection in the second molecule with 'index ' followed
by the numbers you just extracted.
then you can get a list of the the velocity components via 'get {x y z}'.

after that you delete velocity selection(s) move all one frame ahead
and start again.


PS> Thanks in advance
PS> Philipp

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.