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.
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.
Hello Jakub Hryc ,
For the last part of the question, I have seen a lot of literature (and GROMACS manual also) where hydrogen is not used for order parameter calculation.They use Ci+1 Ci-1 definition.
Quantitatively order parameter shows us the orderedness of lipid molecules, therefore using either definition leads to same scientific conclusion. Though the original definition uses hydrogen atom but in simulation, carbon or deuterium is used probably because they are heavy atoms.
For the first part, perhaps you need to write a code as gromacs probably does not use hydrogen atom for order parameter calculation.
Lastly if you want to compare simulation with experiments, compare the middle atoms and see if they match (with a reasonable range of difference).
I am new in this area, so I am following this thread for further and detailed clarification. Thank you.
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