SV: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel

[Sarah Witzke]

Thank you for your quick respons! It is not so much the drop, but more the position and the prescens of a small drop, then a little rise and then the big drop. I have pasted the file in below.
Do you think my method of replacing the order parameters for the double bonded atoms is ok?
 
****************Order parameters sn-2 chain POPC*********
           1       0.176177
           2        0.18184
           3       0.182874
           4       0.180724
           5       0.167932
           6       0.162731
           7       0.107512
           8       0.139351
           9      0.0311607
          10      0.0519802
          11       0.095191
          12      0.0884555
          13      0.0930531
          14      0.0787042
          15      0.0732823
          16      0.0541174

******************************************************************
 
Thank you, Sarah

________________________________

Fra: gmx-users-bounces at gromacs.org på vegne af Justin A. Lemkul
Sendt: to 25-02-2010 14:42
Til: Discussion list for GROMACS users
Emne: Re: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel





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
>

--
========================================

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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