> But now for the most important question: is there a reproducible problem > with the angle?
Yes. I include everything into a tar: http://biocroma.unizh.ch/gianluca/Files/Gromacs/hbond.tar.bz2 I'm using the following command to verify if the hydrogen bond "ARG 552 HH12 - GLN 548 OE1" is formed along the trajectory: g_hbond -f trajectory.trr -s topol.tpr -r 0.27 -a 60 -n select.ndx -noda -nonitacc -hbm -hbn -nomerge File "hbmap.xpm" tells me that the hbond is formed in only three frames. However, if I plot the distance with g_dist and the angle with g_angle as a function of time (see dist.xvg and angaver.xvg) the distance between hydrogen and acceptor is below 0.27 nm in 61% of the frames and the angle (ADH) is below 60 degrees in almost all frames. All used commands are in the file "commands". Thanks a lot for your help, Gianluca ----------------------------------------------------- Dr. Gianluca Interlandi [EMAIL PROTECTED] +1 (206) 685 4432 +1 (206) 714 4303 http://biocroma.unizh.ch/gianluca/ Postdoc at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. ----------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
