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

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.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:21 CST