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,
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...
-- Bjoern Olausson Martin-Luther-Universität Halle-Wittenberg Fachbereich Biochemie/Biotechnologie Kurt-Mothes-Str. 3 06120 Halle/Saale Phone: +49-345-55-24942
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:49 CST