From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Dec 13 2006 - 11:30:51 CST
(You should just be careful that if you have a TM protein, you also
properly solvate it's interior, which may require a third step or a
different tool)
L. Michel Espinoza-Fonseca wrote:
> ha! It sounds like a nice (and smart) trick.
>
> Thanks!
> Michel
>
> 2006/12/13, 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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