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bond/react:another edge atom clarification

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jrgissing
2019-09-08 22:59:59 -06:00
parent 2e0fcac744
commit 450f437d9f
1 changed files with 13 additions and 11 deletions
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doc/src/fix_bond_react.txt
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@ -188,17 +188,19 @@ Some atoms in the pre-reacted template that are not reacting may have
missing topology with respect to the simulation. For example, the
pre-reacted template may contain an atom that, in the simulation, is
currently connected to the rest of a long polymer chain. These are
referred to as edge atoms, and are also specified in the map file.
When the pre-reaction template contains edge atoms, not all atoms,
bonds, charges, etc. specified in the reaction templates will be
updated. Specifically, topology that involves only atoms that are 'too
near' to template edges will not be updated. The definition of 'too
near the edge' depends on which interactions are defined in the
simulation. If the simulation has defined dihedrals, atoms within two
bonds of edge atoms are considered 'too near the edge.' If the
simulation defines angles, but not dihedrals, atoms within one bond of
edge atoms are considered 'too near the edge.' If just bonds are
defined, only edge atoms are considered 'too near the edge.'
referred to as edge atoms, and are also specified in the map file. All
pre-reaction template atoms should be linked to a bonding atom, via at
least one path that does not involve edge atoms. When the pre-reaction
template contains edge atoms, not all atoms, bonds, charges, etc.
specified in the reaction templates will be updated. Specifically,
topology that involves only atoms that are 'too near' to template
edges will not be updated. The definition of 'too near the edge'
depends on which interactions are defined in the simulation. If the
simulation has defined dihedrals, atoms within two bonds of edge atoms
are considered 'too near the edge.' If the simulation defines angles,
but not dihedrals, atoms within one bond of edge atoms are considered
'too near the edge.' If just bonds are defined, only edge atoms are
considered 'too near the edge.'
NOTE: Small molecules, i.e. ones that have all their atoms contained
within the reaction templates, never have edge atoms.