[gmx-users] gmx gangle in the development version of gromacs

LIANG Xujun Xujun.LIANG at cea.fr
Thu Apr 16 11:33:17 CEST 2015

Dear Eric.

I am now also calculating the angle between normal vector of plane 1 and com vector of plane 1 and plane 2. I also use the following command you used in the mail (with small modifications).

>>gmx gangle -f file.trr -s file.tpr -n  file.ndx -g1 plane -group1 'z 0 to 1
and group a_plane' -g2 z -oh file.xvg -binw 1.0

However, I wonder if the –g1 plane –group1 group a plane could indicate that we want the normal of the plane, when –g2 is set as vector. Since 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 in advance!


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