Action: S2CM

Module	s2cm
Description	Usage
S2 contact model CV.
output value	type
the value of the CV	scalar

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
METHYL_ATOM	atoms	the methyl carbon atom of the residue (i)
NH_ATOMS	atoms	the hydrogen atom of the NH group of the residue (i) and carbonyl oxygen of the preceding residue (i-1)
HEAVY_ATOMS	atoms	the heavy atoms to be included in the calculation

Further details and examples

Text from manual goes here

Syntax

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
METHYL_ATOM	input	none	the methyl carbon atom of the residue (i)
NH_ATOMS	input	none	the hydrogen atom of the NH group of the residue (i) and carbonyl oxygen of the preceding residue (i-1)
HEAVY_ATOMS	input	none	the heavy atoms to be included in the calculation
R_EFF	compulsory	none	the effective distance, r_eff in the equation, given in nm
PREFACTOR_A	compulsory	none	the prefactor, a in the equation
EXPONENT_B	compulsory	none	the exponent, b in the equation
OFFSET_C	compulsory	none	the offset, c in the equation
N_I	compulsory	none	n_i in the equation
NUMERICAL_DERIVATIVES	optional	false	calculate the derivatives for these quantities numerically
NOPBC	optional	false	ignore the periodic boundary conditions when calculating distances
SERIAL	optional	false	Perform the calculation in serial - for debug purpose
NLIST	optional	false	Use a neighbour list to speed up the calculation
NL_CUTOFF	optional	not used	The cutoff for the neighbour list
NL_STRIDE	optional	not used	The frequency with which we are updating the atoms in the neighbour list
R_SHIFT	optional	not used	shift all distances by given amount