[gmx-users] Reliability about Lipid Order Parameters in GROMACS

[Justin Lemkul]

On 9/3/15 3:40 PM, Rebeca García Fandiño wrote:
> Dear GROMACS users
>
> I have a general doubt
> about the reliability of calculating order parameters for lipids containing saturated and
> unsaturated chains. For example, DOPC (attached). The order parameters
> for the two chains are too similar and however one of them is saturated and the other one unsaturated.
>
>
>
> If you notice the
> paper J. Chem. Theory Comput., 2012, 8 (11), pp
> 4593–4609 (http://pubs.acs.org/doi/full/10.1021/ct3003157),
> the authors determined deuterium order parameters using locally written code because
> the GROMACS program g_order did not provide the correct order parameters for
> carbons in the unsaturated double bond of the POPC oleoyl tail (versions 4.0.7
> and 4.5.1 of g_order were tested). I have tried version GROMACS 4.6.2  and
>   GROMACS 5.0 for my DOPC system and the
> results are very similar between both versions, so I think this supposed
>   error has not been corrected in the new versions of GROMACS.
>
>
> Could anyone clarify
> if Deuterium Order parameters are well calculated for the unsaturated double
> bond of lipids in GROMACS?

Try the patch here:

http://redmine.gromacs.org/issues/1166

But no, there has been no action on this issue in many years.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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