VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 22 2010 - 15:45:47 CST

Hi,
  Yes, you can do this, however since a DCD file must contain a
consistent set of atoms, you'll get atoms in the resulting file that
may have originally started within 5A and ultimately drift beyond that
point by the end of the trajectory. If you make no special effort to
create a selection that incorporates the "within 5" results for every
frame, you'll also get "holes" in your trajectory where you are missing
some of the atoms within the 5A distance. Depending on whether or not
this matters to you, you could either just use a "within" selection in the
File->Save Coordinates menu, subsequently writing a new trajectory, or
you could write a Tcl script that computes the set of all water atoms that
ever enter within 5A of the solute, and use those results to save out the
new trajectory.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 22, 2010 at 03:39:54PM -0600, snoze pa wrote:
> Dear VMD users,
>
> I did a NAMD simulation and want to remove all water molecule which
> are more than 5A away from the main protein. Is it possible to do it
> through a tcl script which can remove all water molecule in DCD file
> and retain only water molecules which are only 5A away from the
> protein.
>
> Thank you
> s 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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