Reassign temp

From: Marcelo Puiatti (marcelo.puiatti_at_gmail.com)
Date: Wed Jun 17 2009 - 15:27:18 CDT

Dear all:

I'm trying to perform a couple of MD runs varying the temperature from
50 K to 300 K.
I've read the manual and I add this lines to the config file:

reassignFreq 100
reassignTemp $temperature
reassignIncr 5
reassignHold 300

but after I read the output file with the Namd-plot pluggin with VMD
the system is always at the final temperature.

I'll apreciate any help, I attached here a copy of my config file.

Thank's in advance

Marcelo

#############################################################
## JOB DESCRIPTION ##
#############################################################

coordinates ../ntv.pdb
outputName heat1

set temperature 300

# Continuing a job from the restart files
if {1} {
set inputname min-3
binCoordinates $inputname.restart.coor
# binVelocities $inputname.restart.vel ;# remove the
"temperature" entry if you use this!
extendedSystem $inputname.restart.xsc
}

firsttimestep 2500

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

paraTypeCharmm off
paratypeXplor off
amber on
parmfile ../adri.top
ambercoor ../adri.crd # chequear

# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
temperature $temperature

# Periodic Boundary Conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {0} {
cellBasisVector1 25. 0. 0.
cellBasisVector2 0. 25.3 0.
cellBasisVector3 0. 0. 24.3
cellOrigin -0.14 0.40 -0.39
}
wrapWater on
wrapAll on

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5

# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20

#PME (for full-system periodic electrostatics)
if {0} {
PME yes
PMEGridSizeX 32
PMEGridSizeY 32
PMEGridSizeZ 32
}

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens

# Escalar la temperatura de 0 K a 300K
reassignFreq 100
reassignTemp $temperature
reassignIncr 5
reassignHold 500

# Constant Pressure Control (variable volume)
if {1} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 50.
langevinPistonTemp $temperature
}

restartfreq 1000 ;# 1000steps = every 1ps
dcdfreq 1000
xstFreq 1000
outputEnergies 100
outputPressure 100

# Fixed Atoms Constraint (set PDB beta-column to 1)
if {0} {
fixedAtoms on
fixedAtomsFile nottails.fix.pdb
fixedAtomsCol B
fixedAtomsForces on
}

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

# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)

constraints on
consexp 3
consref ../adri-ntv.pdb
conskfile ../adri-ntv.pdb
conskcol O

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

# Minimization
if {0} {
minimize 1000
reinitvels $temperature
}

run 50000 ;# 0.050 ns

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