Dear Eric. I am now also calculate 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.
>>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. I've tried to use 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, could you please tell me how you define the normal vector of a plane? Betst, Xujun -- 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 [email protected].
