Re: simulation of membrane-protein systems

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Dec 13 2006 - 11:16:21 CST

Hi Michel,
when working with a system that has a bilayer, I usually solvate in two
steps -- one adding water to everything at or above the head groups of
the "top" leaflet, and the other adding water at or below the "bottom"
leaflet, so that the bilayer interior receives no added water.
Peter

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 :).
>
> 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!
>
> Michel
>
> 2006/12/13, Marcos Sotomayor <sotomayo_at_ks.uiuc.edu>:
>>
>> 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 <petefred_at_ks.uiuc.edu>:
>> >>> 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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