lammps/doc/dihedral_helix.txt

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)

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dihedral_style helix command :h3
dihedral_style helix/omp command :h3

[Syntax:]

dihedral_style helix :pre

[Examples:]

dihedral_style helix
dihedral_coeff 1 80.0 100.0 40.0 :pre

[Description:]

The {helix} dihedral style uses the potential

:c,image(Eqs/dihedral_helix.jpg)

This coarse-grain dihedral potential is described in "(Guo)"_#Guo.
For dihedral angles in the helical region, the energy function is
represented by a standard potential consisting of three minima, one
corresponding to the trans (t) state and the other to gauche states
(g+ and g-).  The paper describes how the A,B,C parameters are chosen
so as to balance secondary (largely driven by local interactions) and
tertiary structure (driven by long-range interactions).

The following coefficients must be defined for each dihedral type via the
"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:

A (energy)
B (energy)
C (energy) :ul

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Styles with a {cuda}, {gpu}, {omp}, or {opt} suffix are functionally
the same as the corresponding style without the suffix.  They have
been optimized to run faster, depending on your available hardware, as
discussed in "Section_accelerate"_Section_accelerate.html of the
manual.  The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.

These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
packages, respectively.  They are only enabled if LAMMPS was built with
those packages.  See the "Making LAMMPS"_Section_start.html#start_3
section for more info.

You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.

See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.

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[Restrictions:]

This dihedral style can only be used if LAMMPS was built with the
MOLECULAR package (which it is by default).  See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.

[Related commands:]

"dihedral_coeff"_dihedral_coeff.html

[Default:] none

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:link(Guo)
[(Guo)] Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).