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

**URL:** <https://gromacs.bioexcel.eu/t/is-it-possible-to-compute-order-parameter-in-gromacs-but-for-some-atoms-in-lipid-headgroup/2414>\
**Category:** User discussions\
**Created:** [June 26, 2021, 3:51pm UTC](https://gromacs.bioexcel.eu/t/is-it-possible-to-compute-order-parameter-in-gromacs-but-for-some-atoms-in-lipid-headgroup/2414 "2021-06-26T15:51:14Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![JakubH](https://avatars.discourse-cdn.com/v4/letter/j/df788c/32.png) [@JakubH](https://gromacs.bioexcel.eu/u/JakubH)\
**Post date:** [June 26, 2021, 3:51pm UTC](https://gromacs.bioexcel.eu/t/is-it-possible-to-compute-order-parameter-in-gromacs-but-for-some-atoms-in-lipid-headgroup/2414/1 "2021-06-26T15:51:14Z")

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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](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/392398a1b7f95426aa24c2072968a012d2d003aa.jpeg)  
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)](https://pubs.rsc.org/en/content/articlelanding/2013/cp/c2cp42738a#!divAbstract) - 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](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/b2a41f60080944f25b123f999d4947c1b94709ec.jpeg)  
Then I choose only atoms that I am interested and then I have  
 ![headgroup_whole_only_ok](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/6e72e5e7e2f3cca7b41994551acddd34b061434a.jpeg)  
My results have some differences and I don’t know that this way to calculate the order parameter for headgroup is ok?

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**Author:** ![TomPiggot](https://avatars.discourse-cdn.com/v4/letter/t/77aa72/32.png) [@TomPiggot](https://gromacs.bioexcel.eu/u/TomPiggot)\
**Post date:** [June 28, 2021, 8:12am UTC](https://gromacs.bioexcel.eu/t/is-it-possible-to-compute-order-parameter-in-gromacs-but-for-some-atoms-in-lipid-headgroup/2414/2 "2021-06-28T08:12:02Z")

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

Tom

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**Author:** ![JakubH](https://avatars.discourse-cdn.com/v4/letter/j/df788c/32.png) [@JakubH](https://gromacs.bioexcel.eu/u/JakubH)\
**Post date:** [June 28, 2021, 11:43am UTC](https://gromacs.bioexcel.eu/t/is-it-possible-to-compute-order-parameter-in-gromacs-but-for-some-atoms-in-lipid-headgroup/2414/3 "2021-06-28T11:43:59Z")

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Thank you, I will check