[gmx-users] GMX 5.0.4 gmx gangle to choose the normal vector of a plane

[LIANG Xujun]

Dear GROMACS users,

I am now using gromacs 5.0.4 to calculate the angle between the normal vector of a plane 1 and the COM (center of mass) vector of plane 1 and plane 2, I used the following command:

gmx gangle -f *.xtc -s *.tpr -n *.ndx -g1 plane -group1 plane 1 (I tried to use this command to select the normal vector of plane 1, but it doesn't work!!) -g2 vector -group2 "com of group 1 plus com of group 2" (use this to define the COM vector) -oav *.xvg

But unfortunately, the results I obtained were the angle between plane 1 and COM vector, not normal vector of plane 1 with COM vector. Thus, couly you please help me to define the plane normal vector in gromacs 5.0.4??

Thanks very much in advance!

Sincerely yours,
Xujun