Calculation of Diffusion coefficient

From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Mon Jan 29 2018 - 08:01:13 CST

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

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