diff --git a/doc/molecule.html b/doc/molecule.html index 0f73a4647a..5014f93ab6 100644 --- a/doc/molecule.html +++ b/doc/molecule.html @@ -261,6 +261,8 @@ appears, the Special Bond Counts section must also appear. If this section is not specied, the atoms in the molecule will have no special bonds.
+Shake Flags section:
Shake Atoms section:
See the fix shake doc page for a further description of SHAKE clusters.
+Shake Bond Types section:
This section is only needed when molecules created using the template will be constrained by SHAKE via the "fix shake" command. The other diff --git a/doc/molecule.txt b/doc/molecule.txt index 24871ec0dc..6df436200c 100644 --- a/doc/molecule.txt +++ b/doc/molecule.txt @@ -258,6 +258,8 @@ appears, the Special Bond Counts section must also appear. If this section is not specied, the atoms in the molecule will have no special bonds. +:line + {Shake Flags} section: one line per atom @@ -278,6 +280,8 @@ clusters. 3 = part of a 3-atom SHAKE cluster with two bonds 4 = part of a 4-atom SHAKE cluster with three bonds :ul +:line + {Shake Atoms} section: one line per atom @@ -312,11 +316,13 @@ and b,c,d = IDs of other three atoms bonded to the central atom. See the "fix shake"_fix_shake.html doc page for a further description of SHAKE clusters. +:line + {Shake Bond Types} section: one line per atom line syntax: ID a b c -a,b,c = bond types of bonds in cluster :ul +a,b,c = bond types (or angle type) of bonds (or angle) in cluster :ul This section is only needed when molecules created using the template will be constrained by SHAKE via the "fix shake" command. The other