Methanol - Autocorrelation of total dipole moment

From: Chathurika Abeyrathne (c.abeyrathne_at_student.unimelb.edu.au)
Date: Sat Jun 25 2011 - 03:36:06 CDT

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Hi,

I created a methanol box with a length of 11 A, using VEGA ZZ.
NAMD configurations are as follows:

set temperature 300

structure Methanol.psf
coordinates Methanol.pdb
outputname Methanol
binaryoutput no
paraTypeCharmm on
parameters par_all22_prot.inp
parameters par_all22_vega.inp
dielectric 12.16

#Force field parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 5.5
switching on
switchdist 5.0 ; # should be less than cutoff
pairlistdist 7.8 ; # should be greater than cutoff

#Integrator parameters
margin 0.0
stepspercycle 20

#Output and restart frequencies
restartfreq 100
dcdfreq 100
xstFreq 100
outputEnergies 100
outputPressure 100

# Constant Temperature Control
temperature $temperature ;# if velocity file is used on restart
disable this
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature ;# target temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Constant Pressure Control (variable volume)
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature

#Rotating Constraints
constraints on
consref Methanol.pdb
conskfile Methanol.pdb
conskcol O ;# capital "o" for occupancy column
rotConstraints on
rotConsAxis 0 0 1
rotConsPivot 0 0 0
rotConsVel 0.002 ;# in degrees/step

# Periodic Boundary Conditions
cellBasisVector1 11.0 0.0 0.0
cellBasisVector2 0.0 11.0 0.0
cellBasisVector3 0.0 0.0 11.0
cellOrigin 0.000000 0.000000 0.000000
wrapAll on

#run minimization
minimize 1000

reinitvels $temperature ;# if velocity file is used on
restart disable this

#run
run 80000

Then I found the total dipole moment from VMD and calculated the normalized
autocorrelation of total dipole moment manually.
This varies between +1 and -1 with the time.
Autocorrelation function of total dipole moment should exponentially
decrease to zero.
Is there something wrong with NAMD configuration?

Thank you.

Regards,
Chathurika.

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