	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 [101], based on NH order parameter from [147] and methyl order parameter from [93]. Input parameters can be found in the relevant papers.

Examples

Glossary of keywords and components

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