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minor doc clarification

This commit is contained in:
Jacob Gissinger 2020-08-27 14:53:09 -04:00
parent ab90493e5b
commit 32aede7769
1 changed files with 9 additions and 8 deletions
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doc/src/fix_bond_react.rst
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@ -441,14 +441,15 @@ The constraint of type 'RMSD' has the following syntax:
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