Re: simulation of membrane-protein systems

From: Marcos Sotomayor (
Date: Wed Dec 13 2006 - 11:34:22 CST

On Wed, 13 Dec 2006, L. Michel Espinoza-Fonseca wrote:

> Thank you for your comments.
> I think I wrote that I was measuring the size of the lipid bilayer,
> but I was wrong. I'm indeed measuring the distance of the whole box
> (water+lipid), but I wrote the opposite :).

Michel, if you are measuring the size of the box with the minmax command
of VMD, DO NOT include the lipids in your selection, as the outcome will
give you a box that's bigger in the xy plan that what it really is and
you will have a gap between periodic images that will be filled with water.

> About the answer, yes, I guessed this behavior is not right, specially
> because I don't want to simulate "floating discs" (i.e., a
> lipid-protein system fully surrounded by water). When I build my
> original system it looks good -no waters are found at the edges. Right
> now I'm re-equilibrating everything and hope to get the right results
> this time.

Check your periodic images with VMD first, you may save some time by
setting a smaller box in the xy plane.

> Now that this topic was raised, I was wondering how to add more water
> to your lipid-protein-water system with "solvate". Usually, when I do
> the following:
> solvate mypsf.psf mypdb.pdb -o myoutput -b 3.5 +z 20 -z 20
> But I still get some water molecules in the edges. Maybe you have some
> hints about how to avoid that!

Peter's hint is quite good. You can also use the regular solvate over the
whole system and then delete the water molecules at the edges using a tcl
script. A tutorial on how to do this and how to simulate membrane proteins
will be released soon.


> Michel
> 2006/12/13, Marcos Sotomayor <>:
>> 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.
>> Marcos
>> 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
>> >>>
>> >>
>> >

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