[gmx-users] Order parameter for unsaturated lipid chain in UA model

[Justin A. Lemkul]

Sarah Witzke wrote:
> Dear gmx users,
> 
>  
> 
> I am sorry to ask this question again, but reading in the email achieve did not enlighten me. I found this email which describes my problem, but unfortunately it has no replies:
> 
> http://lists.gromacs.org/pipermail/gmx-users/2008-July/034950.html 
> 
> Also there are these two recently emails: http://lists.gromacs.org/pipermail/gmx-users/2010-January/047767.html <http://lists.gromacs.org/pipermail/gmx-users/2010-January/047767.html> , but I am still in doubt.
> 
> So my question is regarding the unsaturated lipid chain of POPC. I would like to calculate the order parameters for my united atoms so I make first an index file with the tail atoms from the carbonyl-C to the methyl-C and then I run g_order -od. Then I make a new index file with the two atoms of the double bond and the atom before and after the double bond (four atoms in total) running g_order -unsat -od
> 
> I then take the two values from the last g_order run and replace them with the order parameters for the double bond calculated without -unsat. When looking at the graph and comparing to the literature this graph it looks wrong: First there is a small dip in the order for the atom before the double bond, then it goes a bit up for the first double bonded C, and then for the next double bonded C and the atom after that the order is quite low. I know this description is not good, but it was just to explain, that the graph is not as expected.
> 
> I would very much appreciated if anyone could tell me, where I go wrong.
> 

I don't see why a drop in the order parameter is unexpected.  I see it all the 
time in published papers of unsaturated lipids, for example:

http://pubs.acs.org/doi/abs/10.1021/jp902131b
http://www3.interscience.wiley.com/journal/114209721/abstract

-Justin

>  
> 
> Thank you,
> 
> Sarah 
> 

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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