GROMACS version: 2019.4

GROMACS modification: Yes/No

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Dear gromacs users.

I need to calc S^2 order parameters using rotacf for comparison, but i don’t know how to use these data for calculate S^2, can anyone help me?

GROMACS version: 2019.4

GROMACS modification: Yes/No

Here post your question

Dear gromacs users.

I need to calc S^2 order parameters using rotacf for comparison, but i don’t know how to use these data for calculate S^2, can anyone help me?

Hi,

It depends which order parameter you want to calculate. If you want to calculate S^2 order parameter using Lipari Szabo approach, for example as it was done in for C-H bond in biomolecules (JCTC, 2006))

you can use gmx rotacf with the following options

gmx rotacf -f xtc_file ( note rotation and translation should be remove in advance) -s tpr_file

-n index_file (one group with all the vector of interest) -P 2 (second order legendre) -noaver -d (use vector) -o (you get an output with a C_I(t) for each vector in the group)

then S^2=limCI(t) for t-> inf or you can fit the first part of each of C(I) with a function (b+(1-b)exp(-t/te) where b=S^2

Kind regards

Alessandra