abnormal water surface after nvt and npt for POPC membrane

From: pxq ѩ (pxq_at_dicp.ac.cn)
Date: Tue Oct 27 2009 - 19:57:58 CDT

namd-lHello everyone,

I am trying to do a MD simulation of POPC lipid membrane according to the reference. However, I am getting a strange results here.
 
When doing the npt, the water moleculars shrink allow the Z axes while the surface of POPC lipid change a little.

When doing a nvt,the water moleculars get an abnormal surface ( it seams the eight angles were cutoff ) still the surface of popc lipid again change a little.

Besides, I made this water box wtih VMD and simulate it with NAMD, FF Amber 99SB and GAFF.

Following are the scripts of the simulation, attantched are the pictures of both npt and nvt output coordinate.

Waiting for your replay and suggestions is greatly welcomed.

###########################################################################
## JOB DESCRIPTION NPT SIMULATION ##
###########################################################################

#output filed

# preparation for MD simulation
set M 0
set N 1-p
set temperature 300
set begin 0

#############################################################
## Required parameters for each simulation ##
#############################################################

#amber force field parameters
amber yes
parmfile 3emlpopccww-cio2.prmtop
ambercoor 3emlpopccww-cio2.inpcrd
outputname gpcr$N
readexclusions no

# frequencies
outputEnergies 1000
restartfreq 1000

# Force-Field Parameters
exclude scaled1-4
1-4scaling 0.833333
#according to amber
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5

# Periodic Boundary conditions
if {1} {
#change according to volume change with lipid membrane
cellBasisVector1 108. 0. 0.
cellBasisVector2 0. 122. 0.
cellBasisVector3 0. 0 113.
cellOrigin 0.1 -0.3 4.3
}
wrapWater on
wrapAll on

#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSizeX 120
PMEGridSizeY 128
PMEGridSizeZ 120
#PMEGridSpacing 1
}

###################################################
#################for MD simulations################
###################################################

if {1} {

#
timestep 1
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
rigidDieOnError on

#
firsttimestep $begin

#
temperature $temperature

#
dcdfile gpcr$N.dcd
dcdfreq 1000
}

# Continuing a job from the restart files
if {0} {
set inputname gpcr$M
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;
extendedSystem $inputname.restart.xsc
}

# Constant Temperature Control
if {1} {
langevin on ;
langevinDamping 5 ;
langevinTemp $temperature
langevinHydrogen no ;
}

# Constant Pressure Control (variable volume)
if {1} {
useGroupPressure yes ;
useFlexibleCell yes ;
useConstantRatio yes
useConstantArea no ;

langevinPiston on
langevinPistonTarget 1.01325 ;
langevinPistonPeriod 200.
langevinPistonDecay 100.
langevinPistonTemp $temperature
SurfaceTensionTarget 60.0 ;
}

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

# Minimization
if {1} {
minimize 10000
reinitvels $temperature
}

run 2000000 ;# 50ps

>
>
>
>
>

###########################################################################
## JOB DESCRIPTION NPT SIMULATION ##
###########################################################################

#output filed

# preparation for MD simulation
set M 0
set N 1-p
set temperature 300
set begin 0

#############################################################
## Required parameters for each simulation ##
#############################################################

#amber force field parameters
amber yes
parmfile 3emlpopccww-cio2.prmtop
ambercoor 3emlpopccww-cio2.inpcrd
outputname gpcr$N
readexclusions no

# frequencies
outputEnergies 1000
restartfreq 1000

# Force-Field Parameters
exclude scaled1-4
1-4scaling 0.833333
#according to amber
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5

# Periodic Boundary conditions
if {1} {
#change according to volume change with lipid membrane
cellBasisVector1 108. 0. 0.
cellBasisVector2 0. 122. 0.
cellBasisVector3 0. 0 113.
cellOrigin 0.1 -0.3 4.3
}
wrapWater on
wrapAll on

#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSizeX 120
PMEGridSizeY 128
PMEGridSizeZ 120
#PMEGridSpacing 1
}

###################################################
#################for MD simulations################
###################################################

if {1} {

#
timestep 1
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
rigidDieOnError on

#
firsttimestep $begin

#
temperature $temperature

#
dcdfile gpcr$N.dcd
dcdfreq 1000
}

# Continuing a job from the restart files
if {0} {
set inputname gpcr$M
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;
extendedSystem $inputname.restart.xsc
}

# Constant Temperature Control
if {1} {
langevin on ;
langevinDamping 5 ;
langevinTemp $temperature
langevinHydrogen no ;
}

# Constant Pressure Control (variable volume)
if {0} {
useGroupPressure yes ;
useFlexibleCell yes ;
useConstantRatio yes
useConstantArea no ;

langevinPiston on
langevinPistonTarget 1.01325 ;
langevinPistonPeriod 200.
langevinPistonDecay 100.
langevinPistonTemp $temperature
SurfaceTensionTarget 60.0 ;
}

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

# Minimization
if {1} {
minimize 10000
reinitvels $temperature
}

run 2000000 ;# 50ps

              

 ===================================================================================================
 Pang Xueqin
 State Key Laboratory of Molecular Reaction Dynamics
 Dalian Institute of Chemical Physics
 Chinese Academy of Sciences.
 Tel: +86-411-84379352 Fax: +86-411-84675584
 ===================================================================================================

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:25 CST