Re: membrane system

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Wed Sep 21 2011 - 05:02:08 CDT

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

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