S2CM
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 used in [94], based on NH order parameter from [136] and methyl order parameter from [86]. 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