GROMACS modification: No
In gromacs gmx order computes the order parameter per atom for carbon tails. For atom i the vector i-1, i+1 is used together with an axis. then we use this S mol = 1/2(3cos^2 (θ ) − 1),.
So to compute the molecular order parameter for atom for example C3. We need to have indexes for atom C2 and C4 (because we write a vector and check the angle).
But what we should do, when we have the last atom in the tail. For example, I have oleic acid and I want to compute the order parameter for C18? How to do this? I can make an index for C17, but I haven’t C19 (because this atom doesn’t exist in oleic acid), so how can I write a vector? Maybe I should make an index for H atom at the end of the tail???
I ask you because I want to compare results from the simulation of my membrane POPC to these from 1 H– 13 C solid-state nuclear magnetic resonance (NMR) spectroscopy and there they check C-H bond (so they don’t use vector Ci-1 Ci+1 for Ci), so they are able to check this parameter for the last carbon of the tail.
I think its impossible to compute last carbon, because “Note that the order program, by default, numbers the carbon atoms in each chain from 1. It is not possible to compute -SCD for terminal carbon atoms, as they lack neighboring atoms from which the local molecular axis is computed.” http://www.mdtutorials.com/gmx/membrane_protein/09_analysis.html
But I see that people use GROMACS and in the article they have the molecular order parameter for terminal carbon like here https://pubs.rsc.org/en/content/articlehtml/2013/cp/c2cp42738a?casa_token=my-RH0Q6BGwAAAAA:OeeBrgfrlOdwLVUHd7a6YLSuO0xvy2erDtADtmoN4x_nqXmrUwnBE9pcyholDOsPNwTEGXpheDYiTLU (Fig 3 red dots)
And I also have a question.
why in NMR they use CH vector and then in GROMACS they use vector Ci-1 - Ci+1? And they have similar results I don’t get it.
Thank you in advance for your help.