Loading doc/src/Errors_messages.rst +2 −1 Original line number Diff line number Diff line Loading @@ -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. Loading doc/src/fix_bond_react.rst +4 −3 Original line number Diff line number Diff line Loading @@ -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 Loading Loading
doc/src/Errors_messages.rst +2 −1 Original line number Diff line number Diff line Loading @@ -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. Loading
doc/src/fix_bond_react.rst +4 −3 Original line number Diff line number Diff line Loading @@ -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 Loading
