When I calculate the order parameter for lipid molecules I get positive value but many papers reports -SCH value. So is gromacs reporting -SCH values?
You can view here discussion on somewhat opposite:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-November/109695.html
Hi Shakkira! I guess you mean so-called deuterium order parameter. In general in experiments you can obtain absolute values of deuterium order parameters, which are reported then as positive numbers. In simulations you can certainly get even negative values, because there you can precisely determine the direction in which hydrogen atoms are situated. This is not related to any routine in gromacs. You can write even your own code and compute those values according to a known formula for SCD. It is up to you how you want to report them in a paper (the absolute value or a value with the particular sign, which means a direction).
Inna Ermilova . Yes I do wrote a program to calculate the order parameter based on the formula for SCD. When I compared these values with that obtained from gromacs gmx order command i could see difference of a negative sign. So I m confused whether gromacs by default outputs -SCD or not?
Kolattukudy P. Santo
I do happen to see a discussion in Gromacs forum regarding this.
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-December/117577.html
So I guess it gives -Scd although gromacs output file for gmx order does not mention this.
Dear Shakkira, it might depend on what vector you have chosen as a normal to a membrane. It might happen that you have chosen one, and developers used another one due to periodic boundary conditions. This can explain the sign.
Inna Ermilova : I dont think that matters. Cos^2\theta is symmetric about pi/2. So changing the direction of the normal does not affect the scd.
Shakkira Erimban Inna Ermilova : I think that SCD is close to -1/2 (\theta=90 degrees) for chains that are in complete order, the more positive values indicate disorder. So generally presenting -Scd makes sense as -Scd=0. to 0.5 indicate order. The Scd values (3 cos^2 \theta -1)/2 can vary form -0.5 to 1, so negative -scd values are possible.
Kolattukudy P. Santo, it all depends how they wrote it in their code and how Shakkira wrote it. I have seen different variations of such codes.
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