[gmx-developers] Re: g_dist and vsite

Ilya Chorny ichorny at gmail.com
Wed Mar 10 18:51:21 CET 2010

I have been having problems calculating the distance between CA and CB atoms
in ALA using g_dist. The trajectory was run using vsite so the mass of CB in
ALA is set to 0. Since g_dist calculates distances between the center of
mass of the groups if one of the groups has a mass of zero there will be an

I am going to edit gmx_dist as follows. Does anyone see any glaring issues
with doing this?




com[g][d] /= mass[g];


if mass[g] > 0.0
        com[g][d] /= mass[g];

Ilya Chorny Ph.D.
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