Re: system density

From: Jeffrey Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Sun Nov 28 2010 - 20:55:33 CST

I'd like to see a snapshot with the box showing the periodic boundary
conditions and everything folded back into the box. You can do this
with the pbc box commands in VMD.

There are a couple issues. You could simply be calculating the density
wrong, but without seeing the calculation we have no way to know how
you're doing this. The other is that if your protein is large compared
to your simulation cell, it will be very difficult to get the system to
equilibrate to the correct density. In essence, you have a solid mass
that may act to prevent the simulation box from contracting properly.
This is especially true if you are not using anisotropic volume
fluctuations.

It would also be helpful to know how many water molecules you have in
the box and what protein you are working with.
Regards,
     Jeff

On 11/28/2010 1:31 AM, Kwee Hong wrote:
> 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
> <mailto:felmerino_at_uchile.cl> <felmerino_at_uchile.cl
> <mailto: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 <mailto:joyssstan0202_at_gmail.com>
> Fecha: 27-11-2010 08:18
> Para: "namd-l"<namd-l_at_ks.uiuc.edu <mailto: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
>
>
>

-- 
======================================================================
Jeffrey J. Potoff			  jpotoff_at_chem1.eng.wayne.edu
Associate Professor			  Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr			  Phone:(313)577-9357		
Detroit, MI 48202  	                  Fax:  (313)578-5815
http://potoff1.eng.wayne.edu
======================================================================

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