Script Help

From: flavio seixas (oivalf_nix_at_yahoo.com)
Date: Sun May 29 2011 - 18:16:51 CDT

Hi people.

I am trying to run a slow cooling simulate annealing, in which I rapidly rise te temperature to 1000K or 2000K and slowly down to 300K in steps of -25K.

I am using the script below that I found in namd-list but without sucess. The temperature only rises slowly, but dont turns to fall.

Could someone tells me what I am doing wrong?

I will be gratefull for any help.

Flavio

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure PROT_wb.psf
coordinates PROT_wb.pdb

set temperature 300
set outputname PROT_wb_eq

firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters par_all27_prot_lipid_na.inp
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 13.5

# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
cellBasisVector1 86. 0. 0.
cellBasisVector2 0. 100.5 0.
cellBasisVector3 0. 0. 76.0
cellOrigin 70.0 48.0 64.0

wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0

#manual grid definition
#PMEGridSizeX 90
#PMEGridSizeY 105
#PMEGridSizeZ 80

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature

# Output
outputName $outputname
binaryoutput no

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100

#############################################################
## EXTRA PARAMETERS ##
#############################################################

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
minimize 100

reassignTemp 1000

run 500
for { set TEMP 1000 } { $TEMP >= 300 } { incr TEMP -25 } {
  reassignTemp $TEMP
  run 1000
}

minimize 100

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