[gmx-users] Calculating S^2 order parameters using iRED (Isotropic Reorientational Eigenmode Dynamics)

[Bailey A.]

Hi,

I was wondering if anyone has calculated S^2 order parameters using iRED (Isotropic Reorientational Eigenmode Dynamics) in Gromacs and could give me some pointers for where to start?

I've previously calculated S^2 order parameters by averaging the second half of the relaxation curve for each residue as generated by g_rotacf (I'm using version 4.6.4 of Gromacs).

However, I've now been advised to try iRED and I'm struggling to figure out how to calculate the isotropically averaged covariance matrix of the N-H bond vectors, expressed as the 2nd order Legendre polynomial of the angle between the bond vectors, as described in the literature: Prompers, J. J.; Brüschweiler, R. J. Am. Chem. Soc. 2002, 124, 4522- 4534

If anyone can help me get started, I'd be most grateful,

All the best,

Alistair