[gmx-users] A question about deuteriu order parameters graph

[Javier Cerezo]

Hi Alex

Deuterium order parameter is a property related to the relative 
orientation of molecular axis taking the bilayer normal as reference. 
How to use them to extract useful structural information is a matter of 
how you interpret the values regarding their definition (see e.g. 
Egberts and Berendsen [J. Chem. Phys.(1988), vol 89, 3718] or Heller et 
al [J. Phys. Chem. (1993), vol 97, 8343]). In general, by comparing 
order parameters of different systems you can have some hints about the 
phase or ordering of your different systems and how it may change (for 
example at different temperature or after insertion of a membrane protein).

Morover, the usefulness of this paramenter mainly comes from the fact 
that they are readily available from simulations and thus can be used to 
validate your methodology. Concretely, experimental information about 
the deuterium order parameter (Scd, the one you reported) is spread over 
the scientific literature about membranes (see e.g. the series of papers 
from the J.F Nagle's group) and it is the deuterium order parameter 
commonly reported in MD simulations. For the case of DPPC you can take 
for example the ones from Petrache et al [Biophys. J (2000), vol 79, 
3172] and Douliez et al [Biophys. J. (1995), vol 68, 1727]. Take into 
account that GROMACS g_order tool just numerate your atoms in the order 
the order parameters are calculated: the first Scd comes from the second 
atom in the index, per the calculation procedure, so is the CH2 close to 
the carbonyl (normally numbered as 2 in the chain).

In your case, if you compare your graphs with the experimental ones 
(pure bilayers), they are significantly different, which may arise from 
the fact of the protein insertion (I doubt it, however) or indicate an 
incorrect MD calculation (bad parameters, not well converged...) or 
incorrect Scd calculation. Please, post your MD details (FF, mdp 
file...) and how you calculated the Scd to continue the discussion. Did 
you calculate the Scd on the pure bilayer?

Javier


El 08/11/11 06:41, Alex escribió:
> Dear All,
>
> I run a MD simulation on a membrane protein using DPPC and I performed a
> deuterium order parameters on the trajectory.
> As I'm a newbie, could you kindly help me to give an interpretation of these
> graphs?
>
> You can open them at:
> sn1
> http://www.freeimagehosting.net/137c9
>
> sn2
> http://www.freeimagehosting.net/6e321
>
>
> Thanks in advance
>

-- 
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tlf.(+34)868887434