From c2a852ddef1f188e999dc07782c60f8b59683b4a Mon Sep 17 00:00:00 2001 From: jrgissing Date: Sat, 24 Oct 2020 13:46:28 -0400 Subject: [PATCH] clarify exactly what is used to identify reaction site MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit thanks to Øystein Gullbrekken for the suggestion --- doc/src/fix_bond_react.rst | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index 159e39d075..d611a58e96 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -174,10 +174,12 @@ integer. Three physical conditions must be met for a reaction to occur. First, a bonding atom pair must be identified within the reaction distance cutoffs. Second, the topology surrounding the bonding atom pair must -match the topology of the pre-reaction template. Finally, any reaction -constraints listed in the map file (see below) must be satisfied. If -all of these conditions are met, the reaction site is eligible to be -modified to match the post-reaction template. +match the topology of the pre-reaction template. Only atom types and +bond connectivity are used to identify a valid reaction site (not bond +types, etc.). Finally, any reaction constraints listed in the map file +(see below) must be satisfied. If all of these conditions are met, the +reaction site is eligible to be modified to match the post-reaction +template. A bonding atom pair will be identified if several conditions are met. First, a pair of atoms I,J within the specified react-group-ID of type