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: [email protected] 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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