On Mon, Dec 9, 2013 at 12:58 PM, Albert <mailmd2...@gmail.com> wrote:

> Hello:
> I am calculating the water density inside my membrane protein along Z
> directions. I used the a_ri3DC tool in Gridcount which is a patch in
> Gromacs for calculation:
> a_ri3Dc -grid gridxdr.dat -profile profile.xvg -xyp xyp.dat -xzp xzp.dat
> -yzp yzp.dat -rzp rzp.dat -rdf rdf.xvg -zdf zdf.xvg -lzdf lzdf.xvg -hxyp
> hxyp.dat -hrzp hrzp.dat -hrdf hrdf.xvg -dump gridasc.dat
> Then I plot the water density with above generated file: hrzp.dat
> I found that the water density along X direction is symmetric even my
> protein is not symmetric. The water density along Z directions seems to be
> good. Does anybody have any idea what's problem? Why the density in X
> direction is symmetric?
Why shouldn't it be?  Is the density along y symmetric, as well?  I have
never used a_ri3Dc so I don't know what it's doing, what data you're
providing it, or what you should expect, but intuitively, unless a membrane
protein protrudes extensively into the aqueous layer, you are not going to
see any effect on the water density in x or y.




Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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