[gmx-users] How deuterium order parameters computed?

[Reid Van Lehn]

I believe the two approaches you list are identical; the prefactors of 2/3
and 1/3 in the equation specified assume a tetrahedral symmetry. This
relation is often just stated as fact (since it is relatively
straightforward to derive) but there is a nice write up of it by J.-P.
Douliez, A. Ferrarini, and E.-J. Dufourc, "On the relationship between C-C
and C-D order parameters and its use in studying the conformation of lipid
acyl chains in biomembranes", J. Chem. Phys. 109 (1998).

Also note that this same reference shows the correct derivation of the S_CD
order parameter for sp2 symmetry, which is currently incorrect in Gromacs
has been reported previously (see bug report on redmine:
http://redmine.gromacs.org/issues/1166). There has been some previous
discussion on the list for workarounds for this problem if it applies to
you.

Best,
Reid


On Tue, Apr 1, 2014 at 9:42 PM, Bin Liu <fdusuperstring at gmail.com> wrote:

> Hi Everyone,
>
> I have a question about the implementation details of g_order. When I was
> reading literatures, I found several interpretations of how the deuterium
> order parameters are computed. One is calculate S_{ij} first, then
>
> S_{CD} = \frac{2}{3} S_{xx} + \frac{1}{3} S_{yy}.
>
> Another approach is assuming ideal tetrahedral geometry of the C-D bonds
> and the two neighbouring carbons, then reconstruct the coordinates of both
> possible Ds, then take the average of the angles between the C-D bonds and
> the system normal.
>
> I am curious about that if they are equivalent and which approach was
> implemented into GROMACS. It seems the cited paper in g_order.c didn't
> mention either of them.
>
> A new order parameter for tetrahedral configurations P.-L. CHAU and A. J.
> HARDWICK  MOLECULAR PHYSICS, 1998, VOL. 93, NO. 3, 511- 518
>
> Thanks for your clarification.
>
> Bin
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-- 
Reid C. Van Lehn
Alfredo Alexander-Katz Research Group
http://soft-materials.scripts.mit.edu/www/member.shtml?member=reid
Ph.D Candidate - Materials Science