Re: abnormal water surface after nvt and npt for POPC membrane

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Oct 28 2009 - 10:55:16 CDT

On Wed, 2009-10-28 at 08:57 +0800, pxq 庞雪芹 wrote:
> 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.

according to _what_ reference?

> When doing the npt, the water moleculars shrink allow the Z axes while the surface of POPC lipid change a little.

this doesn't sound strange at all. this is equilibration.

> 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.

same thing here. your system seem to have a "safety vacuum" between the
lipids and the water and the bubble just moves into the corner(s). look
at the system with periodic images and you should see.

> 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.

there are no attachments.

> Waiting for your replay and suggestions is greatly welcomed.

please note replay is for sports, reply for email.

cheers,
   axel.

>
> ###########################################################################
> ## 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
> ===================================================================================================
>
>
>
>
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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