Re: Sample Configuratiion files

From: Cheri M Turman (Cheri.M.Turman_at_uth.tmc.edu)
Date: Wed Nov 03 2004 - 19:47:25 CST

Hi Ray,
I think Jim Phillips helped me out with this issue earlier. Thanks to
him, here is a sample from one of my config scripts showing the
simulated annealing part:

for { set TEMP 300 } { $TEMP < 1050 } { incr TEMP 50 } {
 run 250
 reassignTemp $TEMP
}
run 8000
for { set TEMP 1000 } { $TEMP >= 0 } { incr TEMP -20 } {
 run 200
 reassignTemp $TEMP
}
for { set TEMP 0 } { $TEMP < 320 } { incr TEMP 20 } {
 run 10
 reassignTemp $TEMP
}
run 8000

These heat from 300-1000K by 50K steps in 3.5ps, hold at 1000K for 8ps,
slow cool from 1000-0K in 10ps, etc. using a timestep of 1.

Hope this helps!
Cheers
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   Cheri M. Turman
   Graduate Student
   University of Texas-Houston Medical School
    6431 Fannin
    Houston, TX 77030 USA

    e-mail: cheri.m.turman_at_uth.tmc.edu
    Ph.: 713-500-6126
    Fax: 713-500-0652

----- Original Message -----
From: "Raymond C. Fort Jr." <rcfort_at_maine.edu>
Date: Wednesday, November 3, 2004 2:59 pm
Subject: namd-l: Sample Configuratiion files

> 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. rcfort_at_maine.edu
> Department of Chemistry chemistry.umeche.maine.edu/fort.html
> 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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