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@ -13,17 +13,27 @@
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>special_bonds style
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special_bonds c1 c2 c3
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special_bonds c1 c2 c3 c4 c5 c6
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<PRE>special_bonds style args
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</PRE>
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<UL><LI>style = <I>charmm</I> or <I>amber</I>
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<LI>c1,c2,c3,c4,c5,c6 = numeric coefficients from 0.0 to 1.0
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<UL><LI>style = <I>charmm</I> or <I>amber</I> or <I>dihedral</I> or <I>explicit</I> (<I>explicit</I> can be omitted)
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<PRE> <I>charmm</I> args = none
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<I>amber</I> args = none
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<I>dihedral</I> args = c1 c2 c3 c4 c5 c6
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c1,c2,c3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions (and Coulomb if c4,c5,c6 are not specified)
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c4,c5,c6 = weights (0.0 to 1.0) on pairwise Coulomb interactions (optional)
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<I>explicit</I> args = c1 c2 c3 c4 c5 c6
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c1,c2,c3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions (and Coulomb if c4,c5,c6 are not specified)
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c4,c5,c6 = weights (0.0 to 1.0) on pairwise Coulomb interactions (optional)
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</PRE>
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</UL>
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<P>Examples:
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</P>
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<PRE>special_bonds charmm
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special_bonds amber
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special_bonds dihedral 0.0 0.0 0.5
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special_bonds explicit 0 1 1
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special_bonds 0 1 1
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special_bonds 0.0 0.0 1.0 0.0 0.0 0.5
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</PRE>
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@ -31,49 +41,68 @@ special_bonds 0.0 0.0 1.0 0.0 0.0 0.5
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</P>
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<P>Set the weighting coefficients for the pairwise force and energy
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contributions from atom pairs that are also bonded to each other
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directly or indirectly. The 1st coefficient is the weighting factor
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on 1-2 atom pairs, which are those directly bonded to each other. The
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2nd coefficient is the weighting factor on 1-3 atom pairs which are
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those separated by 2 bonds (e.g. the 2 H atoms in a water molecule).
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The 3rd coefficient is the weighting factor on 1-4 atom pairs which
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are separated by 3 bonds (e.g. the 1st and 4th atoms in a dihedral
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directly or indirectly. For Lennard-Jones and Coulombic pairwise
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interactions, the 1st coefficient is the weighting factor on 1-2 atom
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pairs, which are those directly bonded to each other. The 2nd
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coefficient is the weighting factor on 1-3 atom pairs which are those
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separated by 2 bonds (e.g. the 2 H atoms in a water molecule). The
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3rd coefficient is the weighting factor on 1-4 atom pairs which are
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separated by 3 bonds (e.g. the 1st and 4th atoms in a dihedral
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interaction).
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</P>
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<P>Note that for purposes of computing weighted pairwise interactions,
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1-3 and 1-4 interactions are not defined from the list of angles or
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1-3 and 1-4 interactions are NOT defined from the list of angles or
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dihedrals used by the simulation. Rather, they are inferred
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topologically by the set of bonds defined when atoms are read in from
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a file (<A HREF = "read_data.html">read_data</A> or
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<A HREF = "read_restart.html">read_restart</A>). Thus the set of 1-2,1-3,1-4
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interactions is the same whether angle potentials are computed or not,
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and remains the same even if bonds are constrained, or turned off, or
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removed during a simulation. The only exception is if the
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<A HREF = "delete_bonds.html">delete_bonds</A> command is used with the <I>special</I>
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option that recomputes the 1-2,1-3,1-4 topologies; see the command for
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more details.
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interactions is the same whether angle and dihedral potentials are
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computed or not, and remains the same even if bonds are constrained,
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or turned off, or removed during a simulation.
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</P>
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<P>The <I>charmm</I> style sets all 3 coefficients to 0.0, which is the
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default for the CHARMM force field. In pair styles
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<I>lj/charmm/coul/charmm</I> and <I>lj/charmm/coul/long</I> the 1-4 coefficients
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are defined explicitly, and these pair-wise contributions are computed
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in the charmm dihedral style - see the <A HREF = "pair_coeff.html">pair_coeff</A>
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and <A HREF = "dihedral_style.html">dihedral_style</A> commands for more
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information.
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<P>The two exceptions to this rule are (a) if the special_bonds
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<I>dihedral</I> style is used (see below), or (b) if the
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<A HREF = "delete_bonds.html">delete_bonds</A> command is used with the <I>special</I>
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option that recomputes the 1-2,1-3,1-4 topologies after bonds are
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deleted; see the <A HREF = "delete_bonds.html">delete_bonds</A> command for more
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details.
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</P>
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<P>The <I>charmm</I> style sets all 3 coefficients to 0.0 for both LJ and
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Coulombic interactions, which is the default for the CHARMM force
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field. In pair styles <I>lj/charmm/coul/charmm</I> and
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<I>lj/charmm/coul/long</I> the 1-4 coefficients are defined explicitly, and
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these pair-wise contributions are computed in the charmm dihedral
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style - see the <A HREF = "pair_coeff.html">pair_coeff</A> and
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<A HREF = "dihedral_style.html">dihedral_style</A> commands for more information.
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</P>
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<P>The <I>amber</I> style sets the 3 coefficients to 0.0 0.0 0.5 for LJ
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interactions and to 0.0 0.0 0.833 for Coulombic interactions, which is
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the default for a particular version of the AMBER force field, where
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the last value is 5/6.
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interactions and to 0.0 0.0 0.8333 for Coulombic interactions, which
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is the default for a particular version of the AMBER force field,
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where the last value is really 5/6.
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</P>
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<P>For a <A HREF = "units.html">lj units</A> system with <A HREF = "bond_fene.html">FENE bonds</A> a
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setting of special bonds 0 1 1 should be used.
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<P>The <I>dihedral</I> style requires you to set 3 or 6 coefficients (see the
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<I>explicit</I> style), but it turns off the 1-4 weighting factor for
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individual atom pairs if they are not listed as the first and last
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atoms in any dihedral defined in the simulation. For example, imagine
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you have set the 1-4 weighting factor to 0.5 and you have a linear
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molecule with 5 atoms and bonds as follows: 1-2-3-4-5. If your data
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file defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a
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dihedral, then the pairwise interaction between atoms 1 and 4 will be
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weighted by 0.5, but the interaction between atoms 2 and 5 will be
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unaffected (full weighting of 1.0). Note that if any of the other
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special_bond styles are used, then the 2,5 interaction would also be
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weighted by 0.5. The <I>dihedral</I> style is provided because some force
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fields follow this rule.
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</P>
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<P>A special_bonds command with 3 coefficients sets the 1-2, 1-3, and 1-4
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coefficients for both LJ and Coulombic terms to those values.
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<P>The <I>explicit</I> style requires you to set 3 or 6 coefficients directly.
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If 3 are specified, they are used for both LJ and Coulombic
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interactions. If 6 are specified then the first 3 are LJ coefficients
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and the second 3 are Coulombic coefficients. Note that the <I>explicit</I>
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keyword itself is optional; the special_bonds command can just take 3
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or 6 numeric arguments by themselves.
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</P>
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<P>A special_bonds command with 6 coefficients sets the 1-2, 1-3, and 1-4
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LJ coefficients to the first 3 values and the Coulombic coefficients
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to the last 3 values.
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<P>IMPORTANT NOTE: For a <A HREF = "units.html">lj units</A> system with <A HREF = "bond_fene.html">FENE
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bonds</A> a setting of special bonds 0 1 1 should be used.
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</P>
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<P><B>Restrictions:</B> none
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</P>
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@ -10,17 +10,25 @@ special_bonds command :h3
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[Syntax:]
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special_bonds style
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special_bonds c1 c2 c3
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special_bonds c1 c2 c3 c4 c5 c6 :pre
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special_bonds style args :pre
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style = {charmm} or {amber}
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c1,c2,c3,c4,c5,c6 = numeric coefficients from 0.0 to 1.0 :ul
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style = {charmm} or {amber} or {dihedral} or {explicit} ({explicit} can be omitted) :ulb,l
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{charmm} args = none
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{amber} args = none
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{dihedral} args = c1 c2 c3 c4 c5 c6
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c1,c2,c3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions (and Coulomb if c4,c5,c6 are not specified)
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c4,c5,c6 = weights (0.0 to 1.0) on pairwise Coulomb interactions (optional)
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{explicit} args = c1 c2 c3 c4 c5 c6
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c1,c2,c3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions (and Coulomb if c4,c5,c6 are not specified)
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c4,c5,c6 = weights (0.0 to 1.0) on pairwise Coulomb interactions (optional) :pre
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:ule
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Examples:
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special_bonds charmm
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special_bonds amber
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special_bonds dihedral 0.0 0.0 0.5
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special_bonds explicit 0 1 1
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special_bonds 0 1 1
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special_bonds 0.0 0.0 1.0 0.0 0.0 0.5 :pre
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@ -28,49 +36,68 @@ special_bonds 0.0 0.0 1.0 0.0 0.0 0.5 :pre
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Set the weighting coefficients for the pairwise force and energy
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contributions from atom pairs that are also bonded to each other
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directly or indirectly. The 1st coefficient is the weighting factor
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on 1-2 atom pairs, which are those directly bonded to each other. The
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2nd coefficient is the weighting factor on 1-3 atom pairs which are
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those separated by 2 bonds (e.g. the 2 H atoms in a water molecule).
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The 3rd coefficient is the weighting factor on 1-4 atom pairs which
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are separated by 3 bonds (e.g. the 1st and 4th atoms in a dihedral
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directly or indirectly. For Lennard-Jones and Coulombic pairwise
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interactions, the 1st coefficient is the weighting factor on 1-2 atom
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pairs, which are those directly bonded to each other. The 2nd
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coefficient is the weighting factor on 1-3 atom pairs which are those
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separated by 2 bonds (e.g. the 2 H atoms in a water molecule). The
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3rd coefficient is the weighting factor on 1-4 atom pairs which are
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separated by 3 bonds (e.g. the 1st and 4th atoms in a dihedral
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interaction).
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Note that for purposes of computing weighted pairwise interactions,
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1-3 and 1-4 interactions are not defined from the list of angles or
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1-3 and 1-4 interactions are NOT defined from the list of angles or
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dihedrals used by the simulation. Rather, they are inferred
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topologically by the set of bonds defined when atoms are read in from
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a file ("read_data"_read_data.html or
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"read_restart"_read_restart.html). Thus the set of 1-2,1-3,1-4
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interactions is the same whether angle potentials are computed or not,
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and remains the same even if bonds are constrained, or turned off, or
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removed during a simulation. The only exception is if the
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"delete_bonds"_delete_bonds.html command is used with the {special}
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option that recomputes the 1-2,1-3,1-4 topologies; see the command for
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more details.
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interactions is the same whether angle and dihedral potentials are
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computed or not, and remains the same even if bonds are constrained,
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or turned off, or removed during a simulation.
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The {charmm} style sets all 3 coefficients to 0.0, which is the
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default for the CHARMM force field. In pair styles
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{lj/charmm/coul/charmm} and {lj/charmm/coul/long} the 1-4 coefficients
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are defined explicitly, and these pair-wise contributions are computed
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in the charmm dihedral style - see the "pair_coeff"_pair_coeff.html
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and "dihedral_style"_dihedral_style.html commands for more
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information.
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The two exceptions to this rule are (a) if the special_bonds
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{dihedral} style is used (see below), or (b) if the
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"delete_bonds"_delete_bonds.html command is used with the {special}
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option that recomputes the 1-2,1-3,1-4 topologies after bonds are
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deleted; see the "delete_bonds"_delete_bonds.html command for more
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details.
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The {charmm} style sets all 3 coefficients to 0.0 for both LJ and
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Coulombic interactions, which is the default for the CHARMM force
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field. In pair styles {lj/charmm/coul/charmm} and
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{lj/charmm/coul/long} the 1-4 coefficients are defined explicitly, and
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these pair-wise contributions are computed in the charmm dihedral
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style - see the "pair_coeff"_pair_coeff.html and
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"dihedral_style"_dihedral_style.html commands for more information.
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The {amber} style sets the 3 coefficients to 0.0 0.0 0.5 for LJ
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interactions and to 0.0 0.0 0.833 for Coulombic interactions, which is
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the default for a particular version of the AMBER force field, where
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the last value is 5/6.
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interactions and to 0.0 0.0 0.8333 for Coulombic interactions, which
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is the default for a particular version of the AMBER force field,
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where the last value is really 5/6.
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For a "lj units"_units.html system with "FENE bonds"_bond_fene.html a
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setting of special bonds 0 1 1 should be used.
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The {dihedral} style requires you to set 3 or 6 coefficients (see the
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{explicit} style), but it turns off the 1-4 weighting factor for
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individual atom pairs if they are not listed as the first and last
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atoms in any dihedral defined in the simulation. For example, imagine
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you have set the 1-4 weighting factor to 0.5 and you have a linear
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molecule with 5 atoms and bonds as follows: 1-2-3-4-5. If your data
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file defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a
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dihedral, then the pairwise interaction between atoms 1 and 4 will be
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weighted by 0.5, but the interaction between atoms 2 and 5 will be
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unaffected (full weighting of 1.0). Note that if any of the other
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special_bond styles are used, then the 2,5 interaction would also be
|
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weighted by 0.5. The {dihedral} style is provided because some force
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fields follow this rule.
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A special_bonds command with 3 coefficients sets the 1-2, 1-3, and 1-4
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coefficients for both LJ and Coulombic terms to those values.
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The {explicit} style requires you to set 3 or 6 coefficients directly.
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If 3 are specified, they are used for both LJ and Coulombic
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interactions. If 6 are specified then the first 3 are LJ coefficients
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and the second 3 are Coulombic coefficients. Note that the {explicit}
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keyword itself is optional; the special_bonds command can just take 3
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or 6 numeric arguments by themselves.
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A special_bonds command with 6 coefficients sets the 1-2, 1-3, and 1-4
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LJ coefficients to the first 3 values and the Coulombic coefficients
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to the last 3 values.
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IMPORTANT NOTE: For a "lj units"_units.html system with "FENE
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bonds"_bond_fene.html a setting of special bonds 0 1 1 should be used.
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[Restrictions:] none
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