Is it possible to compute order parameter in Gromacs, but for some atoms in lipid headgroup?

GROMACS version: 2020.2
GROMACS modification: No
I have a question. Is it possible to compute order parameters for α, β and γ and also g1, g2 and g3 atoms of POPC lipid headgroup in gromacs?
Or maybe I should create my program to do that?
I know that I will not be able to compute for terminal γ atom. And I must make an index file for atoms

  1. γ (I choose one atom per molecule this in the middle, not all three)
  2. N
  3. β
  4. α
  5. O
  6. P
  7. O
  8. g3
  9. g2
  10. g1
  11. O

I thought that I don’t need to add indexes for P atoms, but without them, I have an error like
WARNING: distance between atoms 26688 and 26690 > 0.3 nm (0.304723). The index file might be corrupt.

I want to compare experimental values (Cholesterol and POPC segmental order parameters in lipid membranes: solid state 1H–13C NMR and MD simulation studies - Physical Chemistry Chemical Physics (RSC Publishing) - figure 3) to my from molecular modeling.
I use gmx order with atoms of the index as above:
gmx order -f eq2.xtc -s eq2.tpr -n headgroup_whole.ndx -nr headgroup_whole.ndx -d z -o headgroup_whole.xvg -b 290000 -e 300000
I get that picture

Then I choose only atoms that I am interested and then I have

My results have some differences and I don’t know that this way to calculate the order parameter for headgroup is ok?

You can’t do this properly in GROMACS. Check out the NMRlipids project, there are scripts you can use from there.


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Thank you, I will check