Re: simulation of membrane-protein systems

From: Cesar Luis Avila (
Date: Wed Dec 13 2006 - 09:14:07 CST

Well, indeed taking minmax from lipid selection is a common mistake. You
should take minmax from water box. This is because of the periodic
nature of the box. When writing the coordinates for the system some of
the lipids that were split in the boundaries get wrapped together
resulting in a wider box for lipids than it really is. Since water
molecules are smaller, they are not affected that much.

L. Michel Espinoza-Fonseca escribió:
> 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!
> Cheers,
> Michel
> 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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