# Re: Calculation of Diffusion coefficient

From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Mon Jan 29 2018 - 10:35:57 CST

Okay, I get that calculating diffusion coefficient may not be of much use
in this context.

Sorry, I didn't get what you meant by this: "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? "

If the PMF is converged, then certainly the net total force would be zero
on my specified variable. Sorry, I didn't check the convergence till now
which I can definitely do by plotting the PMF at the different time point
and see whether it is converged or not. But if I wanna check the
uncertainty of the calculated PMF, I need to have the system force
trajectory file for the calculation of say, mean autocorrelation of force
at the different regime of the RC [ J. Phys. Chem. B, 2015, 119 (3), pp
1129–1151 ]. So, is there any way I can get that now without re-running all
the windows?

On Mon, Jan 29, 2018 at 9:32 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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
>

```--
Souvik Sinha
Research Fellow
Bioinformatics Centre (SGD LAB)
Bose Institute
Contact: 033 25693275
```

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