[gmx-users] A. - Vol. / lipid & associated errors

[Nuno R. L. Ferreira]

On Tuesday 08 June 2004 10:33 pm, Erik Lindahl wrote:
> Hi,
>
> > I'm convinced that you guys, before a production run of a bilayer
> > system,
> > perform an equilibration to get the feeling about the area/volume per
> > lipid.
>
> Definitely. Unfortunately it's not quite so good that we equilibrate
> until a certain predetermined metric has been fulfilled, but rather:
> equilibrate as long as you can afford. Yes, it's stupid in one way, but
> the problem is that no matter how long you equilibrate you can always
> find some properties that require longer timescales to reach
> equilibrium... (think lipid flip-flop on second timescales).
>
> > Can someone give some numbers about the associated property errors
> > between the
> > MD obtained values and the experimental ones? 5 % is good in both
> > properties?
>
> That depends on your forcefield. First, volume/lipid is much more
> well-defined experimentally and show lower fluctuations. However, most
> non-lipid forcefields are up to 20% off on both measures. We developed
> some lipid-specific force fields about 5 years ago that have less than
> 1% error for common lipids, but of course that's not quite comparable
> since we're obviously parameterising for the lipids.

So, if the volume/lipid is experimentally well defined, perhaps I should try 
to equilibrate the membrane till a reasonable value, not expecting to reach 
the experimental area/lipid, which has a greater associated error. 

>
> In general, I would recommend using a lipid-specific force field if you
> are interested in examining and reproducing properties of pure
> bilayers.  On the other hand, if your eventual goal is to use the
> membranes as a solvent for proteins you will probably be quite happy
> with setting the area/lipid to the correct value and the using whatever
> force field you like.

Why the area per lipid and not the V. per lipid, as I "suggested" above?

Yes, the bilayer will be just a "solvent" to a protein.

BTW, if I first equilibrate a membrane in NAreaPT conditions, with zero 
compressibility in the plane (xy) of the membrane (with the correct 
area/lipid), and then give semi or anisotropically freedom in the xy plane, 
will the assimptotically area-volume per lipid will be the "same", if I turn 
the semi or anisotropically freedom in the xy plane at the begining of the 
equilibration? I suppose so.

Regards,
Nuno


-- 
**********************************************
Nuno Ricardo Santos Loureiro da Silva Ferreira
Grupo de Química Biológica 
Departamento Química
Universidade de Coimbra
Portugal
www.biolchem.qui.uc.pt
**********************************************
"Do not worry about your difficulties in maths.
 I can assure you that mine are still greater."
                                   emc2