dihedral_style_helix.txt
5b1f5c520a54lammm-devel

dihedral_style_helix.txt
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			"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)

			:line

			dihedral_style helix 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

			[Restrictions:] none

			[Related commands:]

			"dihedral_coeff"_dihedral_coeff.html

			[Default:] none

			:line

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