From: Leandro Martínez (leandromartinez98_at_gmail.com)
Date: Mon Apr 24 2006 - 07:15:34 CDT
Yo can do a simulated annealing using a script like the one
below in the input namd file. This one is for heating, but
for cooling is the same.
Leandro.
#script: increase temperature in 500K in 10000 steps,
# each step is 1.5 ps long (1000 steps with 1.5 fs
# time-step).
temperature 298.15
rescaleFreq 1000
for { set step 0 } { $step <= 10000 } { incr step } {
set TEMP [ expr 298.15 + 5.*sqrt($step) ]
rescaleTemp $TEMP
run 1000
}
On 4/24/06, L. Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu> wrote:
> Dear all,
>
> I've been looking for some information about running simulated
> annealing of a protein in explicit water with NAMD, but I didn't find
> any information. I would like to know if any of you have tried to
> perform such simulation.
>
> Thanks a lot!
> Michel
>
>
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