Hi all,
I have a system of protein+water+ions.
I measured the minimum distance between one of the ions to the protein.
Afterwards I fitted the trajectory using g_trjconv -fit rot+trans
Did the same mindist again and the graphs are not always identical.
Any suggestions?
I use gromacs 4.0.5 with an octahedron box.
same problem happens when I do trjconv -fit rot but does not happen
when -fit trans.
In VMD I do see a difference in the position of the ion relative to
the protein.
Thanks.
Elad P.
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