2006-09-22 00:22:34 +08:00
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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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2011-10-07 01:32:51 +08:00
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<H3>dihedral_style helix/omp command
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</H3>
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2006-09-22 00:22:34 +08:00
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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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2011-10-07 01:32:51 +08:00
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<HR>
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2011-12-14 04:35:35 +08:00
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<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> suffix are functionally
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the same as the corresponding style without the suffix. They have
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been optimized to run faster, depending on your available hardware, as
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discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A> of the
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manual. The accelerated styles take the same arguments and should
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produce the same results, except for round-off and precision issues.
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2011-10-07 01:32:51 +08:00
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</P>
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<P>These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
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packages, respectively. They are only enabled if LAMMPS was built with
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those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
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section for more info.
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</P>
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<P>You can specify the accelerated styles explicitly in your input script
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2012-01-28 07:39:14 +08:00
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by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
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2011-10-07 01:32:51 +08:00
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switch</A> when you invoke LAMMPS, or you can
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use the <A HREF = "suffix.html">suffix</A> command in your input script.
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</P>
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2011-12-14 04:35:35 +08:00
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<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
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more instructions on how to use the accelerated styles effectively.
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2011-10-07 01:32:51 +08:00
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</P>
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<HR>
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2007-06-25 22:36:36 +08:00
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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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2011-08-27 02:53:00 +08:00
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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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2007-06-25 22:36:36 +08:00
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LAMMPS</A> section for more info on packages.
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2006-09-22 00:22:34 +08:00
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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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