[gmx-users] Re: a question about order parameter of POPC

[Justin A. Lemkul]

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/gmx-users@gromacs.org/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: apourmou at uwo.ca <mailto:apourmou at uwo.ca>

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

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

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