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

Berk Hess gmx3 at hotmail.com
Tue Aug 31 10:22:19 CEST 2010


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.


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

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.

ORNL/UT Center for Molecular Biophysics cmb.ornl.gov

865-241-1537, ORNL PO BOX 2008 MS6309

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