Re: simulation of membrane-protein systems

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Dec 13 2006 - 13:59:27 CST

Since the system is periodic, it is important not to have water on
the lateral edges of the membrane. This would represent a system
with water in the middle of the (extended) bilayer. Looking at the
periodic images in VMD as Marcos, I believe, suggested will show what
your bilayer really "looks" like.

On Dec 13, 2006, at 1:47 PM, regafan_at_usc.es wrote:

> Hello,
> I am working with a system similar to Michael´s and from your
> discussion I have a doubt: is it important not to have water in the
> edges of the complete system (protein+bilayer+water)?
>
> Thanks a lot,
>
> Rebeca García Fandiño
> regafan_at_usc.es
>
>
>
>
>
>
>
> Citando Peter Freddolino <petefred_at_ks.uiuc.edu>:
>
>> 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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