Re: Sample Configuratiion files

From: Charles Danko (
Date: Wed Nov 03 2004 - 15:50:49 CST


To restart the simulation just load the last coordinate and velocity
files from the simulation that you are restarting. The rest of the
file should remail the same. Note that you still have to load
structure, topology, etc.

The lines loading the restart files may look like this:

coordinates restart-file.coor
velocities restart-file.vel

or, if you are saving files in binary,

coordinates ORITIONALFILE.pdb
bincoordinates restart-file.coor
binvelocities restart-file.vel

For some reason, you have to use the coordinates option whenever you
are using the bincoordinates option. However, the bincoordinates are
used, and the coordinates line is ignored. See the manual for any
more information. Others may know better than I about this.

Good luck!

On Wed, 03 Nov 2004 15:59:44 -0500, Raymond C. Fort Jr.
<> wrote:
> I'm repeating an earlier post, and adding to it. We would be extremely
> grateful if someone would share with us example configuration files for:
> (1) restarting a simulation (a power outage crashed us)
> (2) a simulated annealing
> I think we may have arrived successfully at the latter by trial and error,
> but an example would still help.
> Thanks!
> Ray
> Professor Ray Fort Jr.
> Department of Chemistry
> University of Maine Voice: (207)-581-1180
> Orono, ME 04469 FAX: (207)-581-1191
> Computer modeling of organic and biomolecules; chemistry of lignin
> and cellulose

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