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

Rebeca García Fandiño regafan at hotmail.com
Thu Sep 3 21:40:44 CEST 2015

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?
Thanks a lot in advance,
Dr. Rebeca Garcia 
Santiago de Compostela UniversitySpain 		 	   		  

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