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. +atoms in any angle defined in the simulation or as 1,3 or 2,4 atoms in +any dihedral 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 or 1-2-3-4 as a +dihedral, 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 diff --git a/doc/special_bonds.txt b/doc/special_bonds.txt index 3eedd32bc8..e0d2715ae0 100644 --- a/doc/special_bonds.txt +++ b/doc/special_bonds.txt @@ -98,17 +98,18 @@ 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. +atoms in any angle defined in the simulation or as 1,3 or 2,4 atoms in +any dihedral 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 or 1-2-3-4 as a +dihedral, 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