diff --git a/doc/special_bonds.html b/doc/special_bonds.html index 73026d8d36..b8b4a6ad37 100644 --- a/doc/special_bonds.html +++ b/doc/special_bonds.html @@ -17,7 +17,7 @@
amber values = none
charmm values = none
@@ -28,6 +28,7 @@
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions
coul values = w1,w2,w3
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
+ angle value = yes or no
dihedral value = yes or no
extra value = N
N = number of extra 1-2,1-3,1-4 interactions to save space for
@@ -39,7 +40,7 @@
special_bonds amber
special_bonds charmm
special_bonds fene dihedral no
-special_bonds lj/coul 0.0 0.0 0.5 dihedral yes
+special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
special_bonds lj/coul 0 1 1 extra 2
@@ -69,8 +70,8 @@ apply to is the same whether angle and dihedral potentials are
computed or not, and remains the same even if bonds are constrained,
or turned off, or removed during a simulation.
-The two exceptions to this rule are (a) if the dihedral keyword is
-set to yes (see below), or (b) if the
+
The two exceptions to this rule are (a) if the angle or dihedral
+keywords are set to yes (see below), or (b) if the
delete_bonds command is used with the special
option that recomputes the 1-2,1-3,1-4 topologies after bonds are
deleted; see the delete_bonds command for more
@@ -101,6 +102,20 @@ keywords only set either the LJ or Coulombic coefficients. Use both
of them if you wish to set the LJ coefficients to different values
than the Coulombic coefficients.
+The angle keyword allows the 1-3 weighting factor to be ignored for
+individual atom pairs if they are not listed as the first and last
+atoms in any angle defined in the simulation. For example, imagine
+the 1-3 weighting factor is set to 0.5 and you have a linear molecule
+with 4 atoms and bonds as follows: 1-2-3-4. If your data file defines
+1-2-3 as an angle, but does not define 2-3-4 as an angle, then the
+pairwise interaction between atoms 1 and 3 will always be weighted by
+0.5, but different force fields use different rules for weighting the
+pairwise interaction between atoms 2 and 4. If the angle keyword is
+specified as yes, then the pairwise interaction between atoms 2 and
+4 will be unaffected (full weighting of 1.0). If the angle keyword
+is specified as no which is the default, then the 2,4 interaction
+will also be weighted by 0.5.
+
The dihedral keyword allows the 1-4 weighting factor to be ignored
for individual atom pairs if they are not listed as the first and last
atoms in any dihedral defined in the simulation. For example, imagine
@@ -132,6 +147,6 @@ you do not do this, you may get an error when bonds are added.
Default:
All 3 Lennard-Jones and 3 Coulobmic weighting coefficients = 0.0,
-dihedral = no, and extra = 0.
+angle = no, dihedral = no, and extra = 0.