Re: system density

From: Kwee Hong (joyssstan0202_at_gmail.com)
Date: Sun Nov 28 2010 - 00:31:17 CST

Thanks Felipe for the tips.

I had recalculate the density by adding the protein yet I still don get a
value near to 1 but some where 0.64.
Any other insights?

Regards,
Joyce

On Sat, Nov 27, 2010 at 11:08 PM, felmerino_at_uchile.cl
<felmerino_at_uchile.cl>wrote:

> 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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