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

[Justin A. Lemkul]

Sarah Witzke wrote:
> Thank you for looking at the data. I just thought, that it deviated too much
> from published results, but perhaps it is because I have mainly worked with
> saturated lipids. I calculated the order over the last 117 ns of a 167 ns
> trajectory (10 ps between each frames), so there should be sufficient data I
> think. Thank you, Sarah

Did you look at the papers I linked earlier?  Your results look pretty similar 
to the data from those papers, which included both experimental and 
computational information.  If you're not used to unsaturated lipids, have a 
look around the literature - there's lots out there!

-Justin

> 
> ________________________________
> 
> Fra: Justin A. Lemkul [mailto:jalemkul at vt.edu] Sendt: to 25-02-2010 15:14 
> Til: Sarah Witzke Emne: Re: SV: [gmx-users] Order parameter for unsaturated
> lipid chain in UAmodel
> 
> 
> 
> 
> 
> Sarah Witzke wrote:
>> 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?
>> 
> 
> This all looks pretty normal to me, perhaps a little rocky from insufficient 
> sampling?  Usually the curves are a bit smoother, but the plot of these data 
> look very much like the published results for other unsaturated lipids.
> 
> -Justin
> 
>> ****************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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>> 
> 
> -- ========================================
> 
> 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
> 
> ========================================
> 
> 
> 

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

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

========================================