membrane moving up in simulation box

From: kanchi subbarao rao (ksubbu85_at_gmail.com)
Date: Mon Oct 17 2011 - 01:09:17 CDT

dear Namd users,
              I am facing a problem in membrane simulation.I did
minimization and equilibration and after production run (NPT 60ns).
I did with both dppc and popc. In both cases, first up to few ns the
structure is looking good, I observed after nearly 20 ns the bilayer was
moving up slowly. since I use periodic boundary conditions in three
directions , the water in upper leaflet comes to lower leaflet (image PBC)
and after that same thing happens to lipid also.

I checked that density of bilayer system also it is 1.0005, volume come to
constant.I look into area per lipid and order parameter, those are fine.
I can not debug where I am doing mistake.I am attaching my configuration
file below.

if anyone has solution,could you help me.

regards
subbarao kanchi.

set temperature1 323.15

Continuing a job from the restart files
if {1} {
set inputname eq_npt2
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature" entry
if you use this!
extendedSystem $inputname.restart.xsc
}

##############################
###########################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all36_lipid.prm

wrapWater on
wrapAll on

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 11.5
switching on
switchdist 11.0
pairlistdist 12.0

# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20

#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSpacing 1.0
}

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature1

# Constant Pressure Control (variable volume)
if {1} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell yes ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane
useConstantRatio yes ;# yes for x/y ratio fixed
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 50.
langevinPistonTemp $temperature1
}

restartfreq 1000 ;# 1000steps = every 1ps
dcdfreq 1000
xstFreq 1000
outputEnergies 1000
outputPressure 1000

margin 3

run 50000000 ;# 50.0 ns

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