output .coor minus solvation box

From: brosbam_at_berkeley.edu
Date: Wed Jul 30 2008 - 18:27:01 CDT

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 with another tcl
script to get rid of the solvation box. However, if there is a way to do
this without repeatedly restarting NAMD, this would be best because my
perl program is presently waiting for NAMD to finish entirely before
advancing.

Thank you,
Bryan
University of California, Berkeley

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