[gmx-users] on g_potential and lipid bilayer analysis

[Rainer Boeckmann]

Dear Francesco,

did you fit the trajectory on the bilayer before applying g_potential? A thing
not considered in g_potential are bilayer undulations (although small for the
dppc64 system) or protrusions. These will certainly affect the profile. To get a
symmetric profile you'll need very long trajectories (>>1ns) and - perhaps not
for this small system - take undulations and protrusions into account. Or
symmetrize...

cheers,
rainer

Francesco Tordini wrote:

> Dear all,
> i'm trying to simulate an asymmetric membrane, created by
> editing by hand the dppc64 system found on Tieleman's site.
> The first dynamic run was good, and now i'm calculating
> some system properties. I was able to manage order parameters
> (g_order) and atom densities (g_density), but i've noticed
> a strange behavior of the gromacs g_potential tool. At first, i
> addressed the problem to the complexity of my system.
> To check this problem, i've simulated also the pure dppc64 sytem
> in the same conditions of the mixed bilayer. Again the run was good,
> but g_potential can't produce a symmetric profile for the potential
> along the membrane z-direction. Again, the shape of the chart is very
> sensitive to the number of slices used for the calculation.
> For example, for the dppc bilayer, i obtain a symmetric chart
> (as one can expect for a sytem like this) only with 151 slices. Little
> variations of these numbers produce big changes especially on the values
> of the potential in the two acqueous phases, desymmetrizing the data.
> Maybe i'm missing something, but i've read for example (Tieleman &
> Berendsen 1996) that the "data was symmetrized" for the potential chart.
> Moreover, even if g_potential assigns 0 potential to the water phase,
> there is a particular reason for the assignment of zero potential to the
> middle of the bilayer (and than to scale the potential values on the y
> axis, i suppose)? --> (again Tieleman & Berendsen 1996).
> This aspect is important to me, especially for a correct interpretation
> of the asymmetric bilayer properties.
>
> Cheers
>
> Francesco
>
> ------------------------------------------
>
> Dr. Francesco Tordini
> Università di Milano-Bicocca
> Dipartimento di Biotecnologie e Bioscienze
> P.zza della Scienza, 2 - 20126 Milano
> Tel.  0264483473 / Fax. 0264483478
> cell. 3282794451
> email tordini at tiscalinet.it
>
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--
Dr. Rainer Böckmann
Theoretical Molecular Biophysics Group
Max-Planck-Institute for Biophysical Chemistry
Am Faßberg 11
D-37077 Göttingen

tel:    +49(551)201-1141
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email: rboeckm at gwdg.de