Re: Unsure about current setting of Periodic Boundary Conditions

From: Diego Alejandro Vargas (vardiego9_at_gmail.com)
Date: Mon Dec 22 2008 - 08:50:16 CST

Hi all,
I am still having problems with this and wanted to know if anybody had any
input. I tried running the simulation again with wrapWater and wrapAll off
and no extendedSystem file. It is running, but increasingly slow. What is
this a consequence of?

Thank you,
Diego A. Vargas

On Tue, Dec 16, 2008 at 12:09 AM, Diego Alejandro Vargas <
vardiego9_at_gmail.com> wrote:

> Hi everybody,
> I am running a constant velocity pulling of a protein in a water box. When
> looking at the dcd file it appears that after the molecule is pulled partly
> outside the water box, it is scaled down in size and then it shows up at
> another part of the box. This happens again in a later step.
>
> Does this mean periodic boundary conditions are on? Or is it a function of
> how VMD displays the result? I didn't intend there to be periodic boundary
> conditions, but I am unsure about a couple of things in the configuration
> file: Should wrapWater and wrapAll be on? Is there a need for an
> extendedSystem file from the previous equilibration simulation from where
> the protein is obtained? Neither the PME nor the cellBiasVector parameters
> are set, so why would this be occuring?
>
> Below I copy my configuration file in case it may help find the source of
> the problem. It is based on the configuration file in the tutorial for
> pulling on ubiquitin, which states. "There is no need to modify the Periodic
> Boundary Conditions, Force Field Parameters, Integrator Parameters or PME
> sections (The latter is disabled since you are not using periodic boundary
> conditions)."
>
> Thank you for your attention,
> Diego A. Vargas
> _______________________________________________________
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure wt_fascin_wb.psf
> coordinates wt_fascin_wb.pdb
> outputName wt_pcv
>
> set temperature 310
>
> # Continuing a job from the restart files
> if {1} {
> binCoordinates wt_eq.restart.coor
> extendedSystem wt_eq.restart.xsc
> }
>
> firsttimestep 0
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters ../common/par_all27_prot_lipid.inp
>
> temperature $temperature
>
>
> # Periodic Boundary conditions
> # NOTE: Do not set the periodic cell basis if you have also
> # specified an .xsc restart file!
> if {0} {
> cellBasisVector1 20. 0. 0.
> cellBasisVector2 0. 20. 0.
> cellBasisVector3 0. 0 50.
> cellOrigin 0. 0. 0.
> }
> wrapWater on
> wrapAll on
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
> # Constant Temperature Control
> langevin off ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen no ;# don't couple langevin bath to hydrogens
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 500
> xstFreq 500
> outputEnergies 100
> outputPressure 100
>
>
> # Fixed Atoms Constraint (set PDB beta-column to 1)
> if {1} {
> fixedAtoms on
> fixedAtomsFile wt_eq.ref
> fixedAtomsCol B
> }
>
> #############################################################
> ## SMD PARAMETERS ##
> #############################################################
>
> SMD on
> SMDFile wt_eq.ref
> SMDk 4.17312
> SMDVel 0.001
> SMDDir -0.721515427178 -0.373667773982 0.582913272306
>
> SMDOutputFreq 10
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> run 285000
>

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