[gmx-users] why it is symmetric

Justin Lemkul jalemkul at vt.edu
Tue Dec 10 14:47:56 CET 2013

On Mon, Dec 9, 2013 at 12:58 PM, Albert <mailmd2011 at 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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