waterbox changes shape during steered molecular dynamics

From: Mert Gür (gurmert_at_gmail.com)
Date: Mon Jun 21 2010 - 14:13:21 CDT

Dear all,
I am trying to do steered molecular dynamics starting from random
structures in the trajectory.
For that reason I am loading the trajectory to VMD and then simply
save the selected frames as pdb files.
I am using them as initial structures for SMD.
Since I cant use restart files anymore, I am setting the temperature
and the cellBasisvector at the beginning
The waterbox changes its shape significantly during the simulation. I
have attached the snapshot.
I observed such an behaviour only ones when I had forgotten to set the
periodic boundary conditions and the water
approached its minimum energy shape which is a sphere.
Does this make sense to anyone?
Best,
Mert

######################################################
## INPUT AND OUTPUT FILES ##
######################################################

structure ../common/ionized.psf
coordinates smdref550.pdb
set temperature 310
set outputname B52
set restartname res

firsttimestep 0
# Input
paraTypeCharmm on
parameters ../common/par_all27_prot_lipid.inp
temperature $temperature

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

if {1} {
cellBasisVector1 116.0140 0. 0.
cellBasisVector2 0. 70.3120 0.
cellBasisVector3 0. 0 72.9940
cellOrigin 11.1565 -2.1352 2.7055
}
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 1.0
rigidBonds none
nonbondedFreq 1
fullElectFrequency 1
stepspercycle 5

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 120
PMEGridSizeY 72
PMEGridSizeZ 75

# Constant Temperature Control
langevin on
langevinDamping 5
langevinTemp $temperature
langevinHydrogen on

#############################################################
## EXTRA PARAMETERS ##
#############################################################

if {1} {
fixedAtoms on
fixedAtomsFile smdref.pdb
fixedAtomsCol B
}

SMD on
SMDFile smdref.pdb
#Spring constant
SMDk 5
#Bu sayi 15/timestep olacak
SMDVel 0.00001
SMDDir 0.7927 -0.5241 -0.3113
SMDOutputFreq 10

# Output
outputName $outputname
restartName $restartname
outputEnergies 500
outputPressure 500
restartfreq 10000
dcdfreq 500
xstFreq 10000

run 2500000

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