Re: membrane moving up in simulation box

From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Mon Oct 17 2011 - 01:58:17 CDT

Dear Subbarao,

As far as I can tell, there is nothing wrong with what you describe
(unless it is a systematic drift, in which case you may want to try
options like "Zeromomentum", avoid doing single runs that are too long,
or/and avoid multiple time stteping).

The system/membrane will move around and that's normal. Why do you expect
the membrane to be fixed?

A few comments about your conf file: If you are using rigid bonds all,
then you can increase your timestep from 1 to 2 fs. Once your system is
equilibrated, you really shouldn't need "margin 3"

Regards,
Marcos.

On Mon, 17 Oct 2011, kanchi subbarao rao wrote:

> 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.
>
> 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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