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:jalem...@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-boun...@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
========================================
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