GROMACS version:2020.2
GROMACS modification: Yes/No
I wonder whether the newer vrsion of GROMACS calculates order parameter for lipid chains for an ALL-ATOM unsaturated system.
I have read all the gromacs forum and is aware of the confusion prevailing about its usage. The reference papers by Piggot gave me a lot of insight.
I would be thankful if someone kindly address my confusion.
Thanking in advance
You need to use a tool outside of GROMACS. There are many available and these should all work correctly for all-atom lipid tails irrespective of (un)saturation.
You can even fairly easily write your own code to do this calculation should you wish using something like MDAnalysis.
The only thing to note is that some of the available tools will automatically average the two (or three) C-H order parameters for the saturated carbon atoms. This isn’t really a problem unless you’re specifically looking into order parameter splitting or you want better data for carbon 2 in the sn-2 lipid tail. In these cases you should select software that doesn’t average the values.
Cheers
Tom
Thank you so much, Piggot, for your reply. I did calculate the order parameter using MDAnalysis, But for all-atom without unsaturation, I got a smooth plot. But for the unsaturated all-atom system, I got multiple dips wherever the double bonds were present.