All-atom NMA algorithm and scoring function?

[Yazhini arangas]

I have been looking into the algorithm behind all-atom nma function in Bio3d package. I understand that Hinsen et al. (2000) approach is used to derive force field and pair force constant falls by 1/r^6 to calculate hormonic potential energy. On this regards, there are few following queries that I would like to clarify myself thoroughly,

i) For diagonalization of hessian matrix, Is DIMS method used in the function aanma.pdb(s)() as used when rtb option set to TRUE?

ii) Is Overlap score modified version of RWSIP (Root weighted Square Inner Product) score?

iii) How many modes are considered by default for SIP and covsoverlap calculations?

[Xinqiu Yao]

Overlapped with another issue.