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

[Thomas Piggot]

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.