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bond/react: bond-type-checking docs

This commit is contained in:
Jacob Gissinger 2020-08-18 18:12:01 -04:00
parent df497e4853
commit e4ab49c2e5
2 changed files with 6 additions and 4 deletions
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3
doc/src/Errors_messages.rst
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@ -502,7 +502,8 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Bond/react: Unknown section in map file*
Please ensure reaction map files are properly formatted.
*Bond/react: Atom affected by reaction too close to template edge*
*Bond/react: Atom type affected by reaction too close to template edge*
*Bond/react: Bond type affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the map
file. This could cause incorrect assignment of bonds, angle, etc.

7
doc/src/fix_bond_react.rst
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@ -213,9 +213,10 @@ surrounding topology. As described below, the bonding atom pairs of
the pre-reacted template are specified by atom ID in the map file. The
pre-reacted molecule template should contain as few atoms as possible
while still completely describing the topology of all atoms affected
by the reaction (which includes all atoms that change atom type). For
example, if the force field contains dihedrals, the pre-reacted
template should contain any atom within three bonds of reacting atoms.
by the reaction (which includes all atoms that change atom type or
connectivity, and all bonds that change bond type). For example, if
the force field contains dihedrals, the pre-reacted template should
contain any atom within three bonds of reacting atoms.
Some atoms in the pre-reacted template that are not reacting may have
missing topology with respect to the simulation. For example, the