[gmx-users] Calculation of unsaturated deuterium order parameters for POPC

[Justin A. Lemkul]

chris.neale at utoronto.ca wrote:
> Dear Thomas:
> 
> I agree with your conclusions about g_order.
> 
> My usage of the Berger POPC lipids in combination with the g_order 
> command (as per the instructions in 
> http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order ) yields 
> order parameters of 0.193 and 0.051 for the first and second
> carbons in the double bond at 300K. This is similar to but, as expected, 
> slightly larger than the values described in 
> http://www.sciencedirect.com/science/article/pii/S0014579305014365 where 
> they simulated at 310K and also used g_order. I suspect that one could 
> find tens of publications that use g_order and have published similar 
> values. The Poger paper (On the Validation of Molecular Dynamics 
> Simulations of Saturated and cis-Monounsaturated Phosphatidylcholine 
> Lipid Bilayers: A Comparison with Experiment) gives clearly different 
> values for the first carbon in the double bond than is reported by 
> g_order. One probable reason that this has gone unnoticed so long is 
> that there appears to be no experimental oleoyl order parameters -- as 
> far as I know -- if somebody finds them, please post them.
> 

Cited in Klauda:

dx.doi.org/10.1021/bi00338a027

I also found:

dx.doi.org/10.1007/s00249-005-0482-z

-Justin

> I took a look at the source and it is clearly incorrect for the i+1 
> unsaturated partner in a double bond over i->i+1. I have developed a new 
> version of g_order to fix this, but I'd like to test it first. If we 
> could agree on a single .xtc file to analyze and compare our values then 
> that would be great. I can provide you with one of mine (Berger lipids) 
> or you can provide me with one of yours (off-list).
> 
> Thanks,
> Chris.
> 
> 

-- 
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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

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