Re: simulated annealing with explicit water

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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