From: Dong Luo (us917_at_yahoo.com)
Date: Mon Apr 24 2006 - 13:05:31 CDT
Hi Michel,
I am running heat annealing by NAMD all the time.
Instead of using "reassignTemp" as recently mentioned
by others, I'm using "reinitvels" as well as langevin
dynamics to control the temperature and feel kind of
convenient in my case.
Dong
Part of my configuration file is like this:
set TEMP 300
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient
(gamma) of 5/ps
langevinTemp $TEMP
langevinHydrogen off ;# don't couple langevin
bath to hydrogens
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $TEMP
for { set TEMP 320 } { $TEMP <= 580 } { incr TEMP 20 }
{
run 10000
reinitvels $TEMP
langevinTemp $TEMP
langevinPistonTemp $TEMP
}
run 200000
for { set TEMP 560 } { $TEMP >= 300 } { incr TEMP -20
} {
reinitvels $TEMP
langevinTemp $TEMP
langevinPistonTemp $TEMP
run 20000
}
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