forked from lijiext/lammps
85 lines
2.7 KiB
Plaintext
85 lines
2.7 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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dihedral_style helix command :h3
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dihedral_style helix/omp command :h3
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[Syntax:]
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dihedral_style helix :pre
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[Examples:]
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dihedral_style helix
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dihedral_coeff 1 80.0 100.0 40.0 :pre
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[Description:]
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The {helix} dihedral style uses the potential
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:c,image(Eqs/dihedral_helix.jpg)
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This coarse-grain dihedral potential is described in "(Guo)"_#Guo.
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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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The following coefficients must be defined for each dihedral type via the
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"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
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the data file or restart files read by the "read_data"_read_data.html
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or "read_restart"_read_restart.html commands:
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A (energy)
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B (energy)
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C (energy) :ul
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:line
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Styles with a {cuda}, {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in "Section_accelerate"_Section_accelerate.html
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.
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These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
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KOKKOS, USER-OMP and OPT packages, respectively. They are only
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enabled if LAMMPS was built with those packages. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the "-suffix command-line
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switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
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use the "suffix"_suffix.html command in your input script.
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See "Section_accelerate"_Section_accelerate.html of the manual for
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more instructions on how to use the accelerated styles effectively.
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:line
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[Restrictions:]
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This dihedral style can only be used if LAMMPS was built with the
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MOLECULE package (which it is by default). See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info on packages.
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[Related commands:]
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"dihedral_coeff"_dihedral_coeff.html
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[Default:] none
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:line
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:link(Guo)
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[(Guo)] Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
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