Re: simulation of membrane-protein systems

From: Marcos Sotomayor (
Date: Wed Dec 13 2006 - 11:02:37 CST

Cesar is likely right, and you can easily check if the size of your
cell box is OK by showing the periodic images of your system in VMD (if
the periodic cell info is not included in the dcd, use the vmd command
"molinfo top set a xxx", where xxx is the value you set for size of the
periodic cell in the x direction, same thing with b and c for y and z,
respectively; then use the periodic tab in the graphical representations
window to visualize periodic images).

Just to answer your original questions, the behavior you are observing is
not normal (unless you want to simulate a disc), and you should not
observe water molecules going into the hydrophobic region of the membrane
(not even at the edges). You should also check that your initial
condition is right, i.e., you don't have water molecules already at the
edges of your simulation cell at the level of the hydrophobic region of
your membrane.


On Wed, 13 Dec 2006, Cesar Luis Avila wrote:

> 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.
> Regards
> Cesar
> 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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:55 CST