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

User discussions
1

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?
glowa_lipidu
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

headgroup_whole
headgroup_whole792×612 19.4 KB

Then I choose only atoms that I am interested and then I have
headgroup_whole_only_ok
headgroup_whole_only_ok792×612 18.6 KB

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

2

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

Tom

1 Like
3

Thank you, I will check