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?
Thanks, Ilya
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