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
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
