Well, one way is to use g_hbond -contact. It will give you the number of contacts each frame plus some additional information, if that's what you're after. Make sure you use the cvs version of g_hbond, since previous versions did not handle contacts correctly (for some reason, most of my replies on this list seem to end in that very sentence).
On Mon, 2006-08-14 at 06:06 -0700, mahbubeh zarrabi wrote: > Dear gromacs users > How can i calculate the number of contacts during the > MD trajectory in complex(protein-protein)? > best regard > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > gmx-users mailing list [email protected] > 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 -- Erik Marklund, PhD Student, Molecular Biopcysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] _______________________________________________ gmx-users mailing list [email protected] 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
