forked from lijiext/lammps
86 lines
3.1 KiB
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86 lines
3.1 KiB
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>special_bonds command
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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>
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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>
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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 0.0 0.0 1.0
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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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<P><B>Description:</B>
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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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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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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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</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>
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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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</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>
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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>
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "delete_bonds.html">delete_bonds</A>
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</P>
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<P><B>Default:</B>
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</P>
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<PRE>special_bonds 0.0 0.0 0.0
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</PRE>
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</HTML>
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