RE: Simultaneous water and protein minimization

From: Richard Owczarzy (
Date: Wed Nov 18 2009 - 16:52:09 CST

Can you have a LINUX/UNIX script that runs one simulation after another?
Can you submit the script instead of NAMD to the cluster?


-----Original Message-----
From: [] On
Behalf Of
Sent: Wednesday, November 18, 2009 3:58 PM
Subject: namd-l: Simultaneous water and protein minimization

Hi everyone,

When I do simulation for protein, I first solvate my protein and fix its
coordinate and submit the job for water minimization.Then I retrieve the
file, load it to the existing pdb file and save pdb with coordinates
from last
frame of dcd trajectory.
Now I use the coordinates of this pdb in the NAMD configuration file to
protein minimization.So, its a kind of two step process but as I do my
submission to some outside cluster, everytime I have to bring back the
to my CPU and then again load to the outside system which again puts me
to long
Queue. To avoid this I'm trying to modify my configuration file such
that it
first takes the coordinates from fixed pdb and do water minimization and
proceeding that take coordinate from water minimized structure to do
dynamics, all in one step. Has anyone tried this before or is it just
I'm trying to use some if else commands but NAMD doesn't recognize these
I hope my question is understandable and any help will be appreciated.

Thank you

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