Re: coord file output minus solvation box

From: Joshua Adelman (
Date: Thu Jul 31 2008 - 12:05:08 CDT

The best thing to do I think is to just use catdcd with the
appropriate 'index' file to just pull out the protein coordinates from
the trajectory as you write it. You can then set the stride to skip as
many steps as you need.

You can then output into dcd,xyz or whatever format might work best
for your purposes.


On Jul 30, 2008, at 4:21 PM, wrote:

> Hi,
> I am running a script in perl that sets up a protein-pigment
> structure,
> solvates in a box, adds ions, and then runs a NAMD min/equilibration
> followed by calculations on the ouput structure file. Currently, I am
> outputting restart files with appended step #-labels so that I can
> perform
> subsequent calculations on the structure for once every few steps.
> However, my output is then rather large by the time NAMD is done
> (several
> GB) and for my purposes this can't be allowed. I would like to
> either be
> able to ouput smaller files or possibly perform calculations while
> NAMD is
> running so the files already read can be deleted.
> My question, then, is how can I output just the pigment-protein
> coordinates each time, is there something better than using the
> restart
> files? My only thought so far would be to run NAMD till the first
> step-of-interest and then output a .coor file and use VMD to get rid
> of
> the solvation box. However, if there is a way to do this without
> repeatedly restarting NAMD, this would be best.
> Thank you,
> Bryan
> University of California, Berkeley

Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley
Berkeley, CA 94720 USA

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