forked from lijiext/lammps
95 lines
3.4 KiB
HTML
95 lines
3.4 KiB
HTML
<HTML>
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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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<H3>dihedral_style charmm command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>dihedral_style charmm
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</PRE>
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<P><B>Examples:</B>
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</P>
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<PRE>dihedral_style charmm
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dihedral_coeff 1 120.0 1 60 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>The <I>charmm</I> dihedral style uses the potential
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</P>
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<CENTER><IMG SRC = "Eqs/dihedral_charmm.jpg">
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</CENTER>
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<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
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field. This dihedral style can also be used for the AMBER force field
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(see comment on weighting factors below). See <A HREF = "#Cornell">(Cornell)</A>
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for a description of the AMBER force field.
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</P>
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<P>The following coefficients must be defined for each dihedral type via the
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<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example above, or in
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the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
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or <A HREF = "read_restart.html">read_restart</A> commands:
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</P>
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<UL><LI>K (energy)
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<LI>n (integer >= 0)
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<LI>d (integer value of degrees)
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<LI>weighting factor (0.0 to 1.0)
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</UL>
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<P>The weighting factor is applied to pairwise interaction between the
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1st and 4th atoms in the dihedral, which are computed by a CHARMM
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<A HREF = "pair_charmm.html">pair_style</A> with epsilon and sigma values specified
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with a <A HREF = "pair_charmm.html">pair_coeff</A> command. Note that this
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weighting factor is unrelated to the weighting factor specified by the
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<A HREF = "special_bonds.html">special bonds</A> command which applies to all 1-4
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interactions in the system.
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</P>
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<P>For CHARMM force fields, the special_bonds 1-4 weighting factor should
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be set to 0.0. This is because the pair styles that contain "charmm"
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(e.g. <A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long</A>) define extra
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1-4 interaction coefficients that are used by this dihedral style to
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compute those interactions explicitly. This means that if any of the
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weighting factors defined as dihedral coefficients (4th coeff above)
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are non-zero, then you must use a charmm pair style. Note that if you
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do not set the special_bonds 1-4 weighting factor to 0.0 (which is the
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default) then 1-4 interactions in dihedrals will be computed twice,
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once by the pair routine and once by the dihedral routine, which is
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probably not what you want.
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</P>
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<P>For AMBER force fields, the special_bonds 1-4 weighting factor should
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be set to the AMBER defaults (1/2 and 5/6) and all the dihedral
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weighting factors (4th coeff above) should be set to 0.0. In this
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case, you can use any pair style you wish, since the dihedral does not
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need any 1-4 information.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>This dihedral style can only be used if LAMMPS was built with the
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"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
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LAMMPS</A> section for more info on packages.
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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 = "dihedral_coeff.html">dihedral_coeff</A>
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</P>
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<P><B>Default:</B> none
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</P>
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<HR>
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<A NAME = "Cornell"></A>
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<P><B>(Cornell)</B> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
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Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
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</P>
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<A NAME = "MacKerell"></A>
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<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
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Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998).
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</P>
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</HTML>
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