Re: simulation of membrane-protein systems

From: L. Michel Espinoza-Fonseca (
Date: Wed Dec 13 2006 - 08:23:15 CST

Dear Peter and Cesar,

Thank you for your answers.

Peter: Yes, I'm using pressure controls, but instead of
useConstantRatio I'm using useConstantArea... What do you think? Maybe
I should modify this and see what I get. I don't think I'll be a
problem, since my system is actually in the x-y plane.

Cesar: I'm using the x-y dimensions of the lipid to assign the length
of my periodic box, so I think the problem is not actually being
caused by this. Thank you anyway for the reminder!


2006/12/13, Peter Freddolino <>:
> Hi Michel,
> are you using pressure controls? If so, you may want to try adding
> useConstantRatio to keep your x and y cell dimensions identical to each
> other (this assumes that your membrane is in the x-y plane, so you may
> need to rotate your system).
> Peter
> L. Michel Espinoza-Fonseca wrote:
> > Hi people,
> >
> > I have been performing a few simulations of protein-membrane systems
> > using a flexible cell and PBC. I used the "membrane" plugin to build
> > the membranes. I subjected such membranes to minimization and
> > equilibration for a period of 0.5 ns. I get a pretty good equilibrated
> > slab, so no problem there. The "problem" (I really don't know if
> > that's a problem) is that after continuing my simulation for about 10
> > ns, the shape of the lipid bilayer looks more like a "disc" than a
> > "box". Moreover, water molecules start to surround the Z-axis edges of
> > the membrane. Now my question is, is that normal? According to what I
> > believe, it is not. how can I avoid this?
> > All comments are very appreciated.
> >
> > Thanks a lot!
> > Michel

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