Re: simulation of membrane-protein systems

From: Peter Freddolino (
Date: Wed Dec 13 2006 - 07:49:30 CST

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).

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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