	This is part of the s2cm module
	It is only available if you configure PLUMED with ./configure –enable-modules=s2cm . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

S2 contact model CV.

This CV was used in [82], based on NH order parameter from [117] and methyl order parameter from [76]. Input parameters can be found in the relevant papers.

Examples

Glossary of keywords and components

Description of components

By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
.#!value	the value of the CV

The atoms involved can be specified using

METHYL_ATOM	the methyl carbon atom of the residue (i). For more information on how to specify lists of atoms see Groups and Virtual Atoms
NH_ATOMS	the hydrogen atom of the NH group of the residue (i) and carbonyl oxygen of the preceding residue (i-1). For more information on how to specify lists of atoms see Groups and Virtual Atoms
HEAVY_ATOMS	the heavy atoms to be included in the calculation. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Compulsory keywords

R_EFF	the effective distance, r_eff in the equation, given in nm.
PREFACTOR_A	the prefactor, a in the equation
EXPONENT_B	the exponent, b in the equation
OFFSET_C	the offset, c in the equation
N_I	n_i in the equation

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
SERIAL	( default=off ) Perform the calculation in serial - for debug purpose
NLIST	( default=off ) Use a neighbour list to speed up the calculation
NL_CUTOFF	The cutoff for the neighbour list
NL_STRIDE	The frequency with which we are updating the atoms in the neighbour list
R_SHIFT	shift all distances by given amount