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

[Rebeca García Fandiño]

Thanks a lot to everybody for the answers.
I would like to try the patch Justin suggested, however, it is not working today. Do you know if there is any problem with it?

http://redmine.gromacs.org/issues/1166
Thanks a lot for all your help.

Best wishes,

Rebeca.


> To: gmx-users at gromacs.org
> From: jalemkul at vt.edu
> Date: Thu, 3 Sep 2015 16:37:18 -0400
> Subject: Re: [gmx-users] Reliability about Lipid Order Parameters in GROMACS
> 
> 
> 
> 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
> 
> -- 
> ==================================================
> 
> 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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