multiple xtc-groups: only first group written out in .xtc file
I specified 2 xtc-groups, protein and ion and grompp'd without index file. The resulting .xtc trajectory gets loaded on a pdb coordinate file (including both groups) and vmd does not report a missmatch of atomnumbers between coordinate and trajectory.
But, after the first coordinate frame, ions are not visualized anymore, instead one ion is displayed, always fixed at the box edge (0,0,0).
Fix selection of xtc groups not starting at index 0
The code to select atoms to write to the xtc file
only looped over the number of atoms selected for
output rather than all atoms. This meant that xtc
group selections that were not located at the start
of the atom indices would not be written correctly.