[gmx-users] g_dist and vsites

Joe Joe ilchorny at gmail.com
Tue Mar 9 19:16:33 CET 2010

Hi I am trying to post process and xtc trajectory using g_dist. I am trying
to calculate the CA-CB distance of an Alanine residue but I get NAN in all
the distance columns. It works for the other residues I've tried (i.e. SER,
VAL). I am using vsites in my simulation and I think it may have some thing
to do with the way gromacs outputs the CB positions in the xtc file when the
CB is part of the vsite network. Any thoughs?


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