hi all

From: kanchi subbarao rao (ksubbu85_at_gmail.com)
Date: Wed Jun 15 2011 - 04:14:04 CDT

hai to all ,
             I am running a simulation of dppc bilayer in NVT ensemble.but
after equilibration i found the bilayer becomes disorder.
I cont debug where I am doing mistake.
and I am using
                                        * useFlexibleCell yes*
* useConstantArea yes*
* *
is this the mean constant area per head group?

shall anyone help me.

thanks
subbarao kanchi

   #############################################################
## JOB DESCRIPTION ##
#############################################################

# Min. and Eq. dppc_bilayer
# embedded in POPC membrane, ions and water.
# Melting lipid tails. PME, Constant Volume.

#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################

structure /home/subbu/delete/dppc-50ns-c27r-xplor.psf
coordinates /home/subbu/delete/dppc-50ns-c27r.pdb
outputName dppc_bilayermineq-01

set temperature 250

# Continuing a job from the restart files
if {0} {
set inputname dppc_bilayer
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature" entry
if you use this!
extendedSystem $inputname.restart.xsc
}

firsttimestep 0

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

# Input
paraTypeCharmm on
parameters
 /home/subbu/delete/parameters/par_all27_lipid_newfp2-dbond.prm

# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
temperature $temperature

# Periodic Boundary Conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {1} {
cellBasisVector1 70. 0. 0.
cellBasisVector2 0. 70. 0.
cellBasisVector3 0. 0. 80.
cellOrigin 0.2818959 0.00359906186 0.066067412
}
wrapWater on
wrapAll on
useFlexibleCell yes
useConstantArea yes

# 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 20

#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSizeX 70
PMEGridSizeY 70
PMEGridSizeZ 80
}

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature

# Constant Pressure Control (variable volume)
if {0} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell yes ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 50.
langevinPistonTemp $temperature
}

restartfreq 1000 ;# 1000steps = every 2ps
dcdfreq 1000
xstFreq 1000
outputEnergies 50
outputPressure 50

# Fixed Atoms Constraint (set PDB beta-column to 1)
if {0} {
fixedAtoms on
fixedAtomsFile /home/subbu/membrane-tutorial-files/kcsa_popcwi.fix
fixedAtomsCol B
fixedAtomsForces on
}

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

# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)

#############################################################
## EXECUTION SCRIPT ##
#############################################################

# Minimization
if {1} {
minimize 1000
reinitvels $temperature
}
#Heating
for {set TEMP 0} {$TEMP<=250} {incr TEMP 5} {
langevinTemp $TEMP
output md.$TEMP
run 1000;#2ps
}

run 500000 ;# 1.0 ns

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