From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Dec 13 2006 - 11:38:11 CST
This thing about a tcl script to remove such waters sounds good too.
Do you already have it available? It'll be nice if you could share it
with some of us :)
Michel
2006/12/13, Marcos Sotomayor <sotomayo_at_ks.uiuc.edu>:
>
>
>
> On Wed, 13 Dec 2006, 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 :).
>
> Michel, if you are measuring the size of the box with the minmax command
> of VMD, DO NOT include the lipids in your selection, as the outcome will
> give you a box that's bigger in the xy plan that what it really is and
> you will have a gap between periodic images that will be filled with water.
>
> >
> > 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.
>
> Check your periodic images with VMD first, you may save some time by
> setting a smaller box in the xy plane.
>
> >
> > 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!
>
> Peter's hint is quite good. You can also use the regular solvate over the
> whole system and then delete the water molecules at the edges using a tcl
> script. A tutorial on how to do this and how to simulate membrane proteins
> will be released soon.
>
> Marcos
>
> >
> > 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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