From: Leandro Martinez (leandromartinez98_at_gmail.com)
Date: Wed Nov 03 2004 - 15:40:38 CST
Raymond,
Below is a sample input file that contains both the keywords to
restart the simulation and a simulated annealing scheme. To restart
the simulation you need only to set the coordinates and velocities
files as the new initial point (this is done by the bincoordinates and
binvelocities here). The simulated annealing is done in this input
file by a simple tcl loop that changes the scaling temperature each
time.
I hope this helps,
Leandro.
#molecular system
coordinates ./psfgen/protein_ready.pdb
bincoordinates protein_start.coor
binvelocities protein_restart.vel
#Restart
restartname protein_restart
restartfreq 2500
#output
dcdfreq 2500
#protocol
#temperature 418.15
rescaleFreq 100
#script
outputname protein_out
rigidbonds all
for { set TEMP 364.15 } { $TEMP >= 298.15 } { set TEMP [ expr $TEMP - 1.0 ] } {
rescaleTemp $TEMP
run 40000
}
rescaleTemp 298.15
run 5000000
On Wed, 03 Nov 2004 15:59:44 -0500, Raymond C. Fort Jr.
<rcfort_at_maine.edu> 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. 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
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:58 CST