Re: membrane system

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Thu Sep 22 2011 - 03:10:00 CDT

On Wednesday 21 September 2011 18:11:57 ipsita basu wrote:
> Sir, I'll follow your method which like :
> vacuum (Air) - monolayer - water - monolayer - vacuum (Air).
> Can I run this in NPT ensemble?
>
Why not?

> How to create this vaccuam in both side in NAMD. I only find that to
> create empty space just increase the value of the length in that axis,
>
This is it.

> but how to specify +ve or -ve direction in the input?
>
+ve, -ve what do you mean with this?

Input? I don't remember PSF or coor files to contain PBC information.
Do you want to set coordinates for a vacuum space?!?
Or are you talking about the NAMD config file?
If yes, just adjust your PBC setup accordingly to the amount of vacuum you
want to have above the membrane interface.

> On Wed, Sep 21, 2011 at 3:32 PM, Bjoern Olausson
>
> <namdlist_at_googlemail.com> wrote:
> > On Wednesday 21 September 2011 08:30:00 you wrote:
> >> Sorry to disturb you again but I sent you mails before regarding this
> >> problem but didn't get any reply from your end.
> >> I have a membrane monolayer system, to make stable this monolayer I
> >> use vaccuam, and to do this I twice the length of the simulation box
> >> in z direction(membrane normal axis> in cellbasis vector option. But
> >> after 8 to 10 ns the waters are again jumping to the lipid end. Will
> >> you please tell me how to fix this?
> >> Another question is if I use 2D option in cellbasis vector, the can
> >> avoid the water jumping problem, but using 2D it will not be possible
> >> to use PME. Is it okay to run without using PME?
> >> Any kind of help from your end is really needed.
> >> Thanking you,
> >> Ipsita
> >
> > This is an expected outcome...
> >
> > To put it in simple words:
> > Either you apply a force to keep the waters on one side - which is
> > somewhat unnatural - or you just set up a symmetrical system: lipids -
> > water - lipids (mind the lipid orientation towards the water ;-).
> > The latter is probably the most common way to setup a monolayer
> > simulation.
> >
> > But to be honest... google could have told you the same and there are
> > tons of papers dealing with monolayers.
> >
> > I even posted a question not long ago, or better a bug, which was dealing
> > with a monolayer setup crashing NAMD. I described my setup pretty
> > detailed...
> >
> > Cheers,
> > Bjoern
> >
> > --
> > Bjoern Olausson
> > Martin-Luther-Universität Halle-Wittenberg
> > Fachbereich Biochemie/Biotechnologie
> > Kurt-Mothes-Str. 3
> > 06120 Halle/Saale
> >
> > Phone: +49-345-55-24942

-- 
Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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