git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2285 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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</H3>
<P><B>Syntax:</B>
</P>
<PRE>special_bonds style
special_bonds c1 c2 c3
special_bonds c1 c2 c3 c4 c5 c6
<PRE>special_bonds style args
</PRE>
<UL><LI>style = <I>charmm</I> or <I>amber</I>
<LI>c1,c2,c3,c4,c5,c6 = numeric coefficients from 0.0 to 1.0
<UL><LI>style = <I>charmm</I> or <I>amber</I> or <I>dihedral</I> or <I>explicit</I> (<I>explicit</I> can be omitted)
<PRE> <I>charmm</I> args = none
<I>amber</I> args = none
<I>dihedral</I> args = c1 c2 c3 c4 c5 c6
c1,c2,c3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions (and Coulomb if c4,c5,c6 are not specified)
c4,c5,c6 = weights (0.0 to 1.0) on pairwise Coulomb interactions (optional)
<I>explicit</I> args = c1 c2 c3 c4 c5 c6
c1,c2,c3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions (and Coulomb if c4,c5,c6 are not specified)
c4,c5,c6 = weights (0.0 to 1.0) on pairwise Coulomb interactions (optional)
</PRE>
</UL>
<P>Examples:
</P>
<PRE>special_bonds charmm
special_bonds amber
special_bonds dihedral 0.0 0.0 0.5
special_bonds explicit 0 1 1
special_bonds 0 1 1
special_bonds 0.0 0.0 1.0 0.0 0.0 0.5
</PRE>
@ -31,49 +41,68 @@ special_bonds 0.0 0.0 1.0 0.0 0.0 0.5
</P>
<P>Set the weighting coefficients for the pairwise force and energy
contributions from atom pairs that are also bonded to each other
directly or indirectly. The 1st coefficient is the weighting factor
on 1-2 atom pairs, which are those directly bonded to each other. The
2nd coefficient is the weighting factor on 1-3 atom pairs which are
those separated by 2 bonds (e.g. the 2 H atoms in a water molecule).
The 3rd coefficient is the weighting factor on 1-4 atom pairs which
are separated by 3 bonds (e.g. the 1st and 4th atoms in a dihedral
directly or indirectly. For Lennard-Jones and Coulombic pairwise
interactions, the 1st coefficient is the weighting factor on 1-2 atom
pairs, which are those directly bonded to each other. The 2nd
coefficient is the weighting factor on 1-3 atom pairs which are those
separated by 2 bonds (e.g. the 2 H atoms in a water molecule). The
3rd coefficient is the weighting factor on 1-4 atom pairs which are
separated by 3 bonds (e.g. the 1st and 4th atoms in a dihedral
interaction).
</P>
<P>Note that for purposes of computing weighted pairwise interactions,
1-3 and 1-4 interactions are not defined from the list of angles or
1-3 and 1-4 interactions are NOT defined from the list of angles or
dihedrals used by the simulation. Rather, they are inferred
topologically by the set of bonds defined when atoms are read in from
a file (<A HREF = "read_data.html">read_data</A> or
<A HREF = "read_restart.html">read_restart</A>). Thus the set of 1-2,1-3,1-4
interactions is the same whether angle potentials are computed or not,
and remains the same even if bonds are constrained, or turned off, or
removed during a simulation. The only exception is if the
<A HREF = "delete_bonds.html">delete_bonds</A> command is used with the <I>special</I>
option that recomputes the 1-2,1-3,1-4 topologies; see the command for
more details.
interactions 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.
</P>
<P>The <I>charmm</I> style sets all 3 coefficients to 0.0, which is the
default for the CHARMM force field. In pair styles
<I>lj/charmm/coul/charmm</I> and <I>lj/charmm/coul/long</I> the 1-4 coefficients
are defined explicitly, and these pair-wise contributions are computed
in the charmm dihedral style - see the <A HREF = "pair_coeff.html">pair_coeff</A>
and <A HREF = "dihedral_style.html">dihedral_style</A> commands for more
information.
<P>The two exceptions to this rule are (a) if the special_bonds
<I>dihedral</I> style is used (see below), or (b) if the
<A HREF = "delete_bonds.html">delete_bonds</A> command is used with the <I>special</I>
option that recomputes the 1-2,1-3,1-4 topologies after bonds are
deleted; see the <A HREF = "delete_bonds.html">delete_bonds</A> command for more
details.
</P>
<P>The <I>charmm</I> style sets all 3 coefficients to 0.0 for both LJ and
Coulombic interactions, which is the default for the CHARMM force
field. In pair styles <I>lj/charmm/coul/charmm</I> and
<I>lj/charmm/coul/long</I> the 1-4 coefficients are defined explicitly, and
these pair-wise contributions are computed in the charmm dihedral
style - see the <A HREF = "pair_coeff.html">pair_coeff</A> and
<A HREF = "dihedral_style.html">dihedral_style</A> commands for more information.
</P>
<P>The <I>amber</I> style sets the 3 coefficients to 0.0 0.0 0.5 for LJ
interactions and to 0.0 0.0 0.833 for Coulombic interactions, which is
the default for a particular version of the AMBER force field, where
the last value is 5/6.
interactions and to 0.0 0.0 0.8333 for Coulombic interactions, which
is the default for a particular version of the AMBER force field,
where the last value is really 5/6.
</P>
<P>For a <A HREF = "units.html">lj units</A> system with <A HREF = "bond_fene.html">FENE bonds</A> a
setting of special bonds 0 1 1 should be used.
<P>The <I>dihedral</I> style requires you to set 3 or 6 coefficients (see the
<I>explicit</I> style), but it turns off the 1-4 weighting factor 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
you have set the 1-4 weighting factor to 0.5 and you have a linear
molecule with 5 atoms and bonds as follows: 1-2-3-4-5. If your data
file defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a
dihedral, then the pairwise interaction between atoms 1 and 4 will be
weighted by 0.5, but the interaction between atoms 2 and 5 will be
unaffected (full weighting of 1.0). Note that if any of the other
special_bond styles are used, then the 2,5 interaction would also be
weighted by 0.5. The <I>dihedral</I> style is provided because some force
fields follow this rule.
</P>
<P>A special_bonds command with 3 coefficients sets the 1-2, 1-3, and 1-4
coefficients for both LJ and Coulombic terms to those values.
<P>The <I>explicit</I> style requires you to set 3 or 6 coefficients directly.
If 3 are specified, they are used for both LJ and Coulombic
interactions. If 6 are specified then the first 3 are LJ coefficients
and the second 3 are Coulombic coefficients. Note that the <I>explicit</I>
keyword itself is optional; the special_bonds command can just take 3
or 6 numeric arguments by themselves.
</P>
<P>A special_bonds command with 6 coefficients sets the 1-2, 1-3, and 1-4
LJ coefficients to the first 3 values and the Coulombic coefficients
to the last 3 values.
<P>IMPORTANT NOTE: For a <A HREF = "units.html">lj units</A> system with <A HREF = "bond_fene.html">FENE
bonds</A> a setting of special bonds 0 1 1 should be used.
</P>
<P><B>Restrictions:</B> none
</P>

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@ -10,17 +10,25 @@ special_bonds command :h3
[Syntax:]
special_bonds style
special_bonds c1 c2 c3
special_bonds c1 c2 c3 c4 c5 c6 :pre
special_bonds style args :pre
style = {charmm} or {amber}
c1,c2,c3,c4,c5,c6 = numeric coefficients from 0.0 to 1.0 :ul
style = {charmm} or {amber} or {dihedral} or {explicit} ({explicit} can be omitted) :ulb,l
{charmm} args = none
{amber} args = none
{dihedral} args = c1 c2 c3 c4 c5 c6
c1,c2,c3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions (and Coulomb if c4,c5,c6 are not specified)
c4,c5,c6 = weights (0.0 to 1.0) on pairwise Coulomb interactions (optional)
{explicit} args = c1 c2 c3 c4 c5 c6
c1,c2,c3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions (and Coulomb if c4,c5,c6 are not specified)
c4,c5,c6 = weights (0.0 to 1.0) on pairwise Coulomb interactions (optional) :pre
:ule
Examples:
special_bonds charmm
special_bonds amber
special_bonds dihedral 0.0 0.0 0.5
special_bonds explicit 0 1 1
special_bonds 0 1 1
special_bonds 0.0 0.0 1.0 0.0 0.0 0.5 :pre
@ -28,49 +36,68 @@ special_bonds 0.0 0.0 1.0 0.0 0.0 0.5 :pre
Set the weighting coefficients for the pairwise force and energy
contributions from atom pairs that are also bonded to each other
directly or indirectly. The 1st coefficient is the weighting factor
on 1-2 atom pairs, which are those directly bonded to each other. The
2nd coefficient is the weighting factor on 1-3 atom pairs which are
those separated by 2 bonds (e.g. the 2 H atoms in a water molecule).
The 3rd coefficient is the weighting factor on 1-4 atom pairs which
are separated by 3 bonds (e.g. the 1st and 4th atoms in a dihedral
directly or indirectly. For Lennard-Jones and Coulombic pairwise
interactions, the 1st coefficient is the weighting factor on 1-2 atom
pairs, which are those directly bonded to each other. The 2nd
coefficient is the weighting factor on 1-3 atom pairs which are those
separated by 2 bonds (e.g. the 2 H atoms in a water molecule). The
3rd coefficient is the weighting factor on 1-4 atom pairs which are
separated by 3 bonds (e.g. the 1st and 4th atoms in a dihedral
interaction).
Note that for purposes of computing weighted pairwise interactions,
1-3 and 1-4 interactions are not defined from the list of angles or
1-3 and 1-4 interactions are NOT defined from the list of angles or
dihedrals used by the simulation. Rather, they are inferred
topologically by the set of bonds defined when atoms are read in from
a file ("read_data"_read_data.html or
"read_restart"_read_restart.html). Thus the set of 1-2,1-3,1-4
interactions is the same whether angle potentials are computed or not,
and remains the same even if bonds are constrained, or turned off, or
removed during a simulation. The only exception is if the
"delete_bonds"_delete_bonds.html command is used with the {special}
option that recomputes the 1-2,1-3,1-4 topologies; see the command for
more details.
interactions 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 {charmm} style sets all 3 coefficients to 0.0, which is the
default for the CHARMM force field. In pair styles
{lj/charmm/coul/charmm} and {lj/charmm/coul/long} the 1-4 coefficients
are defined explicitly, and these pair-wise contributions are computed
in the charmm dihedral style - see the "pair_coeff"_pair_coeff.html
and "dihedral_style"_dihedral_style.html commands for more
information.
The two exceptions to this rule are (a) if the special_bonds
{dihedral} style is used (see below), or (b) if the
"delete_bonds"_delete_bonds.html 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"_delete_bonds.html command for more
details.
The {charmm} style sets all 3 coefficients to 0.0 for both LJ and
Coulombic interactions, which is the default for the CHARMM force
field. In pair styles {lj/charmm/coul/charmm} and
{lj/charmm/coul/long} the 1-4 coefficients are defined explicitly, and
these pair-wise contributions are computed in the charmm dihedral
style - see the "pair_coeff"_pair_coeff.html and
"dihedral_style"_dihedral_style.html commands for more information.
The {amber} style sets the 3 coefficients to 0.0 0.0 0.5 for LJ
interactions and to 0.0 0.0 0.833 for Coulombic interactions, which is
the default for a particular version of the AMBER force field, where
the last value is 5/6.
interactions and to 0.0 0.0 0.8333 for Coulombic interactions, which
is the default for a particular version of the AMBER force field,
where the last value is really 5/6.
For a "lj units"_units.html system with "FENE bonds"_bond_fene.html a
setting of special bonds 0 1 1 should be used.
The {dihedral} style requires you to set 3 or 6 coefficients (see the
{explicit} style), but it turns off the 1-4 weighting factor 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
you have set the 1-4 weighting factor to 0.5 and you have a linear
molecule with 5 atoms and bonds as follows: 1-2-3-4-5. If your data
file defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a
dihedral, then the pairwise interaction between atoms 1 and 4 will be
weighted by 0.5, but the interaction between atoms 2 and 5 will be
unaffected (full weighting of 1.0). Note that if any of the other
special_bond styles are used, then the 2,5 interaction would also be
weighted by 0.5. The {dihedral} style is provided because some force
fields follow this rule.
A special_bonds command with 3 coefficients sets the 1-2, 1-3, and 1-4
coefficients for both LJ and Coulombic terms to those values.
The {explicit} style requires you to set 3 or 6 coefficients directly.
If 3 are specified, they are used for both LJ and Coulombic
interactions. If 6 are specified then the first 3 are LJ coefficients
and the second 3 are Coulombic coefficients. Note that the {explicit}
keyword itself is optional; the special_bonds command can just take 3
or 6 numeric arguments by themselves.
A special_bonds command with 6 coefficients sets the 1-2, 1-3, and 1-4
LJ coefficients to the first 3 values and the Coulombic coefficients
to the last 3 values.
IMPORTANT NOTE: For a "lj units"_units.html system with "FENE
bonds"_bond_fene.html a setting of special bonds 0 1 1 should be used.
[Restrictions:] none