There is a bug in g_order. It produces -Scd values that are similar to
experimental results and those from other simulations, but they are not correct,
at least in the case of unsaturations. Saturated carbons should be correct, if
I recall. So no, there is no satisfactory answer until the bug is fixed. A
code patch was proposed proposed some time ago, but it has not been officially
implemented.
Please post anything further to gmx-users.
-Justin
Amir Mohsen Pourmousa wrote:
Hi Justin,
I just noticed on the mailing list of GROMACS that you had the same
problem that I have now. The response that you got from one of those
people was not satisfactory (I think it didn't satisfy you either):
http://www.mail-archive.com/[email protected]/msg28555.html
Anyway I am trying to compute the order parameter for POPC. I followed
the instruction on Gromacs manual regarding the double bonds but my
graph is different from those in literature. Did you finally succeed in
obtaining the correct order parameter for the oleoyl acyl chain of POPC
which contains double bonds? If yes, would you tell me how?
Best regards,
Amir-Mohsen Pourmousa
-------
Amir-Mohsen Pourmousa
PhD Candidate of Theoretical Physics,
Dept. of Applied Mathematics, University of Western Ontario
1151 Richmond St. North, London (ON), Canada N6A 5B7
Tel: +1-519-661 2111 extension 88678
Cell: +1-519-854 3331
Email: [email protected] <mailto:[email protected]>
--
========================================
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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