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I want to know the formula and algorithm behind SASA calculation in GROMACS.
I checked the GROMACS formula cite ( Index of /current/reference-manual/analysis ) and did not find any proper formula for SASA.
Additionally, I want to know whether SASA is normalised with increase in the number of monomeric units. If not, how to normalise it?
The algorithm used by the gmx sasa module is described in this paper by Eisenhaber et al., which is also stated on the manual page.
I’m not entirely sure what you mean by “normalized with increase in the number of monomeric units”, but the algorithm has no notion of what exactly it’s calculating the SASA for. If your selection contains several subunits and you want to know the average SASA per subunit, simply dividing by their number should do it.
Thankyou @lmullender