Next: Parameters Up: Order Parameter (Contact Model) Previous: Order Parameter (Contact Model) Contents

####
Theory and implementation

This analysis is based on an analytical relationship for the estimation of the generalized order parameter (see Section 4.2.7.1) of N-H vectors of the protein backbone. It related of the N-H vector of residue i to close contact experienced by the H atom and the carbonyl oxygen of the preceeding residue i-1 with heavy atoms k using the formula:

| (4.199)

where is the distance between the carbonyl oxygen of residue i-1 and heavy atom k and is the distance between the amide proton of residue i and heavy atom k. The parameter b is set to -0.1 which takes into account that order parameters of rigid protein regions typically lie around 0.9. The sum ranges over all heavy atoms k that do not belong to amino acids i and i-1. For more details about this method, please refer to Ref. [73]

Beside the time-dependent defined in Eq; 4.199, nMOLDYN also provide a time-averaged defined as:

| (4.200)

where is the number of selected frames for the analysis.

Next: Parameters Up: Order Parameter (Contact Model) Previous: Order Parameter (Contact Model) Contents