From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Jun 17 2013 - 08:51:20 CDT
> That answered the question why only values in z axis are the same
> (neglecting the sign because it depends on the order of group1 and
> group2 defined). The position in x and y dimension of the ion are
> beyond half the box length. So in this case the different coordinate
> outputs from colvar and dcd file are unavoidable if I want to
> measure the distance between the ion and dummy atom at (0, 0, 0),
Indeed. So if you wish to analyze the trajectory using external tools, it could be simpler to use the first option you had in mind, and enforce position and orientation restraints.
Still, one option to analyze a fully unrestrained trajectory is to use VMD's "RMSD trajectory" tool to fit the macromolecule prior to the analysis, so you obtain the same rotated-translated coordinates available from within the colvars module.
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