Re: questions regarding ABF sampling in a DMPC bilayer

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Jan 30 2012 - 06:49:52 CST

Dear Jrme,

> > Actually what I would like to do now is to model the (unbiased) dynamic
> > behaviour of my colvars.
>
> That is an intrinsically difficult question. A couple of colleagues
> have been thinking hard about it for a while now, and they still don't
> have a clear answer. For now, I would say that using ABF (and the
> whole family of biased methods) essentially means that you give up on
> getting dynamical information.
>
> Is the problem in determining the diffusion coefficients or the accuracy
of the PMF or something completely different? (Perhaps the problem is
choosing the "good"colvar?) If you have a PMF and diffusion coefficients,
then one would naively expect that it should be possible to obtain dynamics
of the system as well.

> You might think of a kind of diffusive dynamics, using
> diffusion coefficients to be determined (see below).
>
>
I hope this will suffice. I will compare this to some experimental
EPR measurements, which depend (among other things) on
the rotational diffusion of the spin label.

The only serious attempt I have made to go back to dynamics based on
> ABF results was in the glycerol-in-GlpF work:
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2186255/
> There is an attempt at predicting a mean first passage time, and
> hence, the channel conductance - I am not really convinced about that
> particular result. The method we used to get position-dependent
> diffusion coefficients is from Gerhard Hummer, it is particularly
> simple and effective.
>
> In this paper you have obtained the diffusion coefficients from a set
of separate simulations (since - if I understand correctly - equation (1)
is only valid if a harmonic bias is applied). But as discussed earlier ABF
does not change diffusion coefficients. So why did you determine
diffusion coefficients from independent separate simulations? Is it
possible to get positional dependant diffusion coefficients directly from
ABF simulations as well?

If at all possible, I'd recommend getting dynamical data from unbiased
> simulations.
>
> Uf, I think this will be quite difficult since the rotational diffusion of
the spin label is so slow in the membrane.

Thank you for your answers and best regards,
Ajasja

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