Re: system density

From: felmerino_at_uchile.cl
Date: Sat Nov 27 2010 - 09:08:28 CST

That is because you are calculating the density of the entire box just based on the water molecules. The huge hole that your protein makes in the solvent should account for "the rest of the density".

best

Felipe

----Mensaje original----

De: joyssstan0202_at_gmail.com

Fecha: 27-11-2010 08:18

Para: "namd-l"<namd-l_at_ks.uiuc.edu>

Asunto: namd-l: system density

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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