GROMACS version: 2018.4

GROMACS modification: No

I have a question. I know that Order Parameter is equal to S=½(3<cos2Θ>-1) and this is segmental order parameter.

Where *Θ* is the angle the particular chain segment makes at a time, *t* , with respect to the bilayer normal. So for example for C5 atom in my lipid I create a vector which start in C4 and end in C6, then I check the angle between this vector and normal yes? But this is segmental order parameter, so GROMACS automaticallly calculate SCD from segmental Order parameter, because SCD is something different yes? This is vector in NMR between C-D. So GROMACS in output aoutomatically recalculate SCD from Smol (I found that Smol = -2SCD for single bonds).

So I have a questions:

- Segmental order parameter is the same as molecular order parameter (Smol), but with different name?
- So GROMACS in output automatically recalculate SCD from Smol (I found somewhere that Smol = -2SCD for single bonds)? When I check man gmx order I found something like that “gmx order can also give all diagonal elements of the order tensor and even calculate the deuterium order parameter Scd (default).” So GROMACS default calculate Scd, because SCD we can compare to experimental values from NMR?