minor doc clarification

where 'RMSD' is the required keyword, and *RMSDmax* is the maximum

root-mean-square deviation between atom positions of the pre-reaction

template and the local reaction site, after optimal translation and

rotation of the pre-reaction template. Optionally, a molecule fragment

(of the pre-reaction template) can be specified by *molfragment*\ .

Only atoms that are part of this molecule fragment are used to

determine the RMSD. A molecule fragment must have been defined in the

:doc:`molecule <molecule>` command for the pre-reaction template. For

example, the molecule fragment could consist of only the backbone

atoms of a polymer chain. This constraint can be used to enforce a

specific relative position and orientation between reacting molecules.

rotation of the pre-reaction template. Optionally, the name of a

molecule fragment (of the pre-reaction template) can be specified by

*molfragment*\ . If a molecule fragment is specified, only atoms that

are part of this molecule fragment are used to determine the RMSD. A

molecule fragment must have been defined in the :doc:`molecule

<molecule>` command for the pre-reaction template. For example, the

molecule fragment could consist of only the backbone atoms of a

polymer chain. This constraint can be used to enforce a specific

relative position and orientation between reacting molecules.

Once a reaction site has been successfully identified, data structures

within LAMMPS that store bond topology are updated to reflect the