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

[Rebeca García Fandiño]

Thank you very much
for your suggestions, Tom.

In fact, Ángel and me
are collaborating in this work :)

We are using AMBER,
not CHARMM, this is why we wanted to know if the error about order
parameters had been corrected in the new versions of GROMACS. 

I will try the patch
Justin suggested before modifying the scripts for AMBER.

Cheers,

Rebeca.



> Date: Fri, 4 Sep 2015 01:05:47 +0100
> From: t.piggot at soton.ac.uk
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Reliability about Lipid Order Parameters in GROMACS
> 
> Hi Rebeca,
> 
> The patch linked to by Justin (provided by Chris Neale) does work fine 
> in my hands (well I tested it for the unsaturated double bond in POPC at 
> least). If you are using the CHARMM36 force field, there is a VMD tcl 
> script out there that can be used. As for the script that was made for 
> the work you linked to, Angel Pineiro (who is also at USC) made this 
> (although if I remember correctly it was pretty slow in calculating the 
> order parameters). I'm sure he'd be happy to share, if you so wished.
> 
> Cheers
> 
> Tom
> 
> On 03/09/15 21:37, Justin Lemkul wrote:
> >
> >
> > 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
> >
> 
> -- 
> Dr Thomas Piggot
> University of Southampton, UK.
> 
> -- 
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