From: regafan_at_usc.es
Date: Wed Dec 13 2006 - 13:47:44 CST
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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