forked from lijiext/lammps
65 lines
1.8 KiB
HTML
65 lines
1.8 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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<HR>
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<H3>dihedral_style helix 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 helix
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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 helix
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dihedral_coeff 1 80.0 100.0 40.0
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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>helix</I> dihedral style uses the potential
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</P>
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<CENTER><IMG SRC = "Eqs/dihedral_helix.jpg">
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</CENTER>
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<P>This coarse-grain dihedral potential is described in <A HREF = "#Guo">(Guo)</A>.
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For dihedral angles in the helical region, the energy function is
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represented by a standard potential consisting of three minima, one
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corresponding to the trans (t) state and the other to gauche states
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(g+ and g-). The paper describes how the A,B,C parameters are chosen
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so as to balance secondary (largely driven by local interactions) and
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tertiary structure (driven by long-range interactions).
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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>A (energy)
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<LI>B (energy)
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<LI>C (energy)
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</UL>
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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#start_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 = "Guo"></A>
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<P><B>(Guo)</B> Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
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</P>
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</HTML>
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