Membrane simulation, Box X,Y enlarge, Z shrink and membrane thickness shrink

From: juan du (
Date: Tue Jun 07 2011 - 18:27:25 CDT

Dear, NAMD users
I am doing membrane simulations at NPT. I use an constraint on the protein
backbone and P atom of lipid. The constraintscaling was set 20 kcal/mol at
the starting point and then gradually released. At the same time, I use
surfacetension parameter and set as 20 dyn/cm. After 3 ns NPT simulation, I
found the X-Y of box increase far from the initial set (from 175 to 720A), Z
(175 to 60A) shrink and the thickness of membrane also shrink (from 35 to
15.5 A). My configration file is as the following. I wonder what's the
problem with my simulation. Did you meet this problem? Thanks for the help!

Juan Du

set targetemp 300.0
set coorfile ../../pro-f-0125.pdb
set laststep ../../heat3/hrst3
#--Input File
coordinates $coorfile
structure ../../pro-f-0125.psf
bincoordinates ${laststep}.coor
binvelocities ${laststep}.vel
extendedSystem ${laststep}.xsc
#--Output File
outputname eqoutb0
restartname eqrstb0
outputEnergies 100
binaryoutput yes
xstFreq 2000
DCDFreq 5000
restartFreq 2000
COMmotion no
timestep 1 ;# 2fs/step
#rigidBonds all ;# needed for 2fs/step
nonbondedFreq 1
fullElectFrequency 2

#--Temperature ReScaling
rescaleFreq 100
#rescaleTemp $temperature
rescaleTemp $targetemp

#--Constant T
langevin on
langevinDamping 1.
langevinTemp $targetemp
langevinHydrogen off ;# do not couple bath to hydrogens
#--Constant P
useGroupPressure yes
useFlexibleCell yes
useConstantArea no
useConstantRatio yes
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar --> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $targetemp
SurfaceTensionTarget 20

PME on
PMETolerance 0.000001
PMEGridSpacing 1.0
constraints on
consexp 2
consref $coorfile
conskfile ../../prot-fix2.cnst ;# force constant value
conskcol B
constraintScaling 20.0 ;# the FC is 20 kcal/mol Angstrom
margin 10

#--parameter file
paraTypeCharmm on
parameters ../../par_all27_prot_lipid.prm
exclude scaled1-4
1-4scaling 1.0
dielectric 1.0
switching on
switchdist 10.0
cutoff 12.0
pairlistdist 14.0 ;# cutoff + 2
stepspercycle 10 ;# follow NAMD configuration file
wrapWater on
wrapAll on
#--simulation time
run 100000

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