[gmx-users] why it is symmetric

Albert mailmd2011 at gmail.com
Mon Dec 9 18:58:31 CET 2013


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?

thank you very much.


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