Re: output .coor minus solvation box

From: Peter Freddolino (
Date: Wed Jul 30 2008 - 23:45:25 CDT

Hi Bryan,
if you're willing to alter your approach a little bit, since namd has a
complete embedded tcl interpreter you can run namd until the first step
of interest, perform whatever processing you want (including calling a
perl script or vmd) *within the namd config file* on the most recently
written restart file, and then continue the namd run without restarting.
This action could, of course, include stripping the file of solvent or
fully analyzing it.
Peter 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 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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