**From:** Souvik Sinha (*souvik.sinha893_at_gmail.com*)

**Date:** Mon Jan 29 2018 - 10:35:57 CST

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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?

Please excuse me being naive about all the intricacies.

Thanks for your quick response.

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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