From 49b5825e8da3fc7caea9fe9cc28a655664e101dc Mon Sep 17 00:00:00 2001 From: jrgissing Date: Thu, 5 Sep 2019 23:50:57 -0600 Subject: [PATCH] bond/react docs tweak: address a common mistake no atom of a small molecule should be specified as an edge atom --- doc/src/fix_bond_react.txt | 29 ++++++++++++++++------------- 1 file changed, 16 insertions(+), 13 deletions(-) diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index 5aff35787d..3fe3d8547e 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -186,19 +186,22 @@ 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 -pre-reacted template may contain an atom that would connect 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.' +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.' + +NOTE: Small molecules, i.e. ones that have all their atoms contained +within the reaction templates, never have edge atoms. Note that some care must be taken when a building a molecule template for a given simulation. All atom types in the pre-reacted template