Simulated Annealing for a polymer

From: Rawan Al Nsour (alnsourra_at_vcu.edu)
Date: Mon Feb 04 2013 - 13:13:54 CST

Dear all,
I am trying to have a simulated annealing process for a polymer. I
want to heat the polymer from 100k to 600k using the NVT ensemble.
then cooling using NPT ensemble.
I attached the nvt conf file
Now in the log file, the simulation shows the increment after each
reassinfreq steps which is fine, but the temperature for the timesteps
in between the the reassinfre stay around the the (set temperature
100) value.
I attached a chart for the timesteps vs Temperature ( for a trial to
heat from 100k to 300k in 2.5ns) it shows how T goes ups and downs. I
want the chart to increase smoothly not up and down.
note: I am using the OPLS force fields so that I used the option.
vdwGeometricSigma yes
. i will post my conf in here just in case the attachment doesnot open
#############################################################
## JOB DESCRIPTION ##
#############################################################

structure 196c64.psf
coordinates 196c64.pdb
outputName SAc64-nvtto600-01

set temperature 100

# Continuing a job from the restart files
if {0} {
set inputname kcsa-popcwi
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature"
entry if you use this!
extendedSystem $inputname.restart.xsc
}

firsttimestep 0

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

# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp

# 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 {1} {
cellBasisVector1 79.0 0.0 0.0
cellBasisVector2 0.0 81.0 0.0
cellBasisVector3 0.0 0.0 79.0
cellOrigin 38.224 -2.006 38.221
}

wrapAll on

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 13.5
margin 5.5
vdwGeometricSigma yes

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

#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSizeX 82
PMEGridSizeY 84
PMEGridSizeZ 82
}

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature

#Temperature Reassignment
if {1} {
reassignFreq 1000 ;# timestep between temperature reassignment
reassignTemp $temperature ;#temperature for equillibration (K)
reassignIncr 0.1 ;# temperature increment for equillibration
reassignHold 600 ;# holding temperature for equllibration
}

# Constant Pressure Control (variable volume)
if {0} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell yes ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 50.
langevinPistonTemp $temperature
}

restartfreq 1000 ;# 1000steps = every 2ps
dcdfreq 1000
xstFreq 1000
outputEnergies 100
outputPressure 100

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

# Minimization
minimize 5000

run 5000000 ;# 5 ns

Best Regards,

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