Re: simulation of membrane-protein systems

From: Peter Freddolino (
Date: Wed Dec 13 2006 - 08:25:07 CST

Hi Michel,
I would highly recommend trying useConstantRatio, since it sounds like
part of the problem is that your lipid patch is slightly too small for
the box you've tried to put it in, and if you fix the area, it may
shrink up slightly (which sounds like the behavior you've described).

L. Michel Espinoza-Fonseca wrote:
> 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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