Hi, The distance component along the O-C bond is the distance between O and the COM of CH3. The distance component perpendicular to the O-C bond is such that the intertia (sum m r^2) of the two masses matches that of the 3 H's.
I can mail you an awk script that automatically determines this from the ff itp files. PS we should automate this in Gromacs, just like the "constraints" mdp option. Berk From: rol...@utk.edu Date: Mon, 30 Aug 2010 20:10:18 -0400 To: gmx-users@gromacs.org Subject: [gmx-users] Distance from heavy atom to Methyl Vsite Hi, how does one calculate the distance from the next heavy atom to the MCH3 virtual site of a methyl group? I have a O-C-H3 and thus need to parameterize the constraint length for MCH3 to the oxygen. I can't find or figure out the formula to compute this. Roland -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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/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/mailing_lists/users.php
-- 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/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/mailing_lists/users.php
