Hey. I'm using Gromacs to simulate a transmembrane-peptide and would like to measure the angle between three residues of the protein. The protein gets during the simulation a kink of about 87°. I would like to measure the real angle of the kink with g_sgangle. So I made an index file and defined two groups with:
a 5|a 248 name 17 group1 and a 248|a 477 name 18 group2 The atom numbers are the C alpha atom of the N terminus, the AS where the kink is located and the C terminus. Now I used g_sgangle to measure the angle between this two groups with: g_sgangle -f md_27nstrjconv.trr -n g_sgangle.ndx -s md_27ns.tpr -oa sg_angle.xvg Then I've chosen group1 and group2 (17 18). The sg_angle.xvg looks like that: @ title "Angle between group1 and group2" @ xaxis label "Time (ps)" @ yaxis label "Angle (degrees)" @TYPE xy 0 0.200158 78.4538 10 0.224148 77.0472 20 0.25729 75.0907 30 0.237989 76.2321 40 0.250923 75.4679 50 0.232999 76.5263 60 0.267666 74.4746 70 0.227826 76.8309 80 0.286902 73.3274 90 0.250226 75.5091 100 0.254623 75.2488 ... So it tells me that Gromacs measured an angle of about 0.2??! Can anyone tell me what I am doing wrong? And what tells me the third column of the .xvg file? Thilo-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists