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?
thank you very much.
Albert
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