Unsure about current setting of Periodic Boundary Conditions

From: Diego Alejandro Vargas (vardiego9_at_gmail.com)
Date: Tue Dec 16 2008 - 00:09:12 CST

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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