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Hi,<br><br>The distance component along the O-C bond is the distance between O and the COM of CH3.<br>The distance component perpendicular to the O-C bond is such that the intertia (sum m r^2)<br>of the two masses matches that of the 3 H's.<br><br>I can mail you an awk script that automatically determines this from the ff itp files.<br><br>PS we should automate this in Gromacs, just like the "constraints" mdp option.<br><br>Berk<br><br><hr id="stopSpelling">From: roland@utk.edu<br>Date: Mon, 30 Aug 2010 20:10:18 -0400<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] Distance from heavy atom to Methyl Vsite<br><br>Hi,<div><br></div><div>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.</div>
<div><br></div><div>Roland<br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a><br>
865-241-1537, ORNL PO BOX 2008 MS6309<br>
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