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 -- ========================================== 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 ========================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.