Fwd: membrane moving up in simulation box

From: kanchi subbarao rao (ksubbu85_at_gmail.com)
Date: Thu Oct 13 2011 - 04:54:15 CDT

---------- Forwarded message ----------
From: kanchi subbarao rao <ksubbu85_at_gmail.com>
Date: Thu, Oct 13, 2011 at 12:24 PM
Subject: namd-l: membrane moving up in simulation box
To: namd-l_at_ks.uiuc.edu

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.

Due to this RMSD going to high value.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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