[gmx-users] Distance from heavy atom to Methyl Vsite

[Berk Hess]

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: roland at utk.edu
Date: Mon, 30 Aug 2010 20:10:18 -0400
To: gmx-users at 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 at 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-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100831/78999d41/attachment.html>