Re: Calculation of Diffusion coefficient

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Jan 29 2018 - 10:02:19 CST

Hi Souvik, FYI you may also want to take a look at the more recent papers
by Jeff Comer regarding computing permeabilities of small molecules across
a bilayer.

For something larger, like a peptide, you are definitely much more bound by
the PMF than by the differences in diffusion coefficient. This may be less
of a problem for you, because the diffusion coefficient changes by less
than an order of magnitude between lipid bilayers and bulk water.

As for recomputing the system force along the trajectory, you do have its
average already computed along the collective variable, given by the PMF
(is it converged?). Computing the system force as a function of time would
only help you in collecting diffusion data during the transient regime
before convergence. Re-running on the single-precision, sparsely collected
trajectories may not be of much help.

How about you simply take the last part of the ABF simulation, where the
biasing force doesn't change much due to convergence, and you assume a net
total force of zero on the variable?

Giacomo

On Mon, Jan 29, 2018 at 9:01 AM, Souvik Sinha <souvik.sinha893_at_gmail.com>
wrote:

> Hi,
>
> Currently, I am estimating a peptide insertion (into membrane) free energy
> profile using ABF. I want to calculate the local diffusion coefficient
> along the reaction coordinate for which I need the estimation of 'time
> autocorrelation function of the fluctuations of the instantaneous forces' *[
> J. Phys. Chem. B, 2011, 115 (49), pp 14704–14712 ]*. Unfortunately, I
> forgot to use the "*outputSystemForce*" option in the *'colvar' *block
> during the ABF simulations.
>
> From a previous thread (*http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2010-2011/2154.html
> <http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2010-2011/2154.html>*),
> I found that taking the assumption of similar force distribution and
> autocorrelation time across different window will certainly narrow the
> rerun option to a single window along a specific RC (for the purpose of
> error analysis). But I think, the autocorrelation function of instantaneous
> force will differ along RC because of the different environment (water to
> lipid bilayer) and that is what, I guess, will be reflected in the values
> of diffusion coefficient along RC. In that case, do I need to rerun all the
> windows with "*outputSystemForce*" option enabled (which is pretty
> troublesome right now)? Is there any post-processing option from which I
> can extract the system force trajectory for all the windows?
>
> Thanks.
> --
> Souvik Sinha
> Research Fellow
> Bioinformatics Centre (SGD LAB)
> Bose Institute
>
> Contact: 033 25693275
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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