Re: simulation of membrane-protein systems

From: L. Michel Espinoza-Fonseca (
Date: Wed Dec 13 2006 - 11:12:13 CST

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 :).

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.

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!


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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