system density

From: Kwee Hong (joyssstan0202_at_gmail.com)
Date: Sat Nov 27 2010 - 05:18:19 CST

Hi.

I have my protein solvate with the solvate plugin in vmd, minimized and
equilibrated.

When I calculated the density of my system, it was just some where around
0.577.

The number of water of my system is calculated as follow in TkCOnsole:
set sel [atomselect top water]
puts [expr [$sel num]/3*18]

The system volume was taken from the NAMD Plot.

Can anyone tell me why this occur and how to tackle this problem?

My config file is as follow:

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

# Equilibration with and without CA restrained

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

structure ionized_4mt2.psf
coordinates ionized_4mt2.pdb

set temperature 300
set inputname 4mt2_wb_press

# Continuing a job from the restart files
# if {0} is true
set rs 0 ;# use restart file? 1 = yes
if {$rs==1} {
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature" entry
if you use this!
extendedSystem $inputname.restart.xsc
}
# Continuing a job but not from restart files
if {$rs==0} {
binCoordinates $inputname.coor
binVelocities $inputname.vel ;# remove the "temperature" entry if you
use this!
extendedSystem $inputname.xsc
}

firsttimestep 0

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

# Input
paraTypeCharmm on
parameters par_all22_prot.inp

outputEnergies 100
outputPressure 100
outputTiming 500
dcdfreq 25
xstFreq 250
restartfreq 500 ;# 500steps = every 1ps

# Integrator Parameters
timestep 2.0 ;# 1fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

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

# Periodic Boundary Conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {0} {
# you get the info to make the following from:
# set sel [atomselect top all]
# cell basis vectors:
# measure minmax $sel # then take the difference
# cellOrigin:
# measure center $sel
#
cellBasisVector1 39.8830 0. 0.
cellBasisVector2 0. 38.5300 0.
cellBasisVector3 0. 0 33.2630
cellOrigin -0.0681 0.39595 0.1661
}
wrapAll on
margin 2.5

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 56
PMEGridSizeY 50
PMEGridSizeZ 60

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

# Constant Pressure Control (variable volume)
if {1} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell no ;# 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 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
}

# Output
outputName 4mt2_wb_eq

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

constraints on
consRef restrain_CA.pdb
consKFile restrain_CA.pdb
consKCol B

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

#equilibrate with CAs restrained
run 10000 ;# 60ps
output equil_ca

#equilibrate without CAs restrained
constraintScaling 0
run 20000
output equil_all

Regards,
Joyce

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