Re: vmd-l: force over selection

From: John Stone (
Date: Thu Mar 23 2006 - 10:26:50 CST

  You can use VMD's atom selection feature to write out PDB files with
the occupancy field of selected atoms set to 1, or you could emit a file
containing a list of atom serial numbers (NAMD counts from 1 IIRC) and
use those in your NAMD job, depending on NAMD feature you end up using
for this. I don't know if there's a way to perform selections within NAMD
itself (implied by "update it every step" in your question below),
you'll have to ask the NAMD guys about that stuff...


On Wed, Mar 22, 2006 at 09:51:46PM -0800, Ioana Cozmuta wrote:
> Hi,
> Is it possible to set up the NAMD configuration file such that it would
> take a selection defined in VMD, update it every step and apply a
> harmonic constraint on that selection? What is the correct way of doing
> it? Does anybody have an example of such a configuration file?
> Thank you,
> Ioana
> --
> Ioana Cozmuta, Ph.D
> Eloret Corporation
> NASA Ames Research Center
> Mail Stop 230-3
> Moffett Field, CA 94035
> phone (650) 604-0993
> e-mail:

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