From: Rukhsar Ali (arukhsar052_at_gmail.com)
Date: Wed Aug 12 2020 - 12:44:55 CDT
Thank you for your email.
I know that the Z-distance projection is the most well-used RC to calculate
permeation events and I get that ABF is not an out-of-equilibrium pulling
experiment. Still, there may have hidden barriers related to peptide
orientation, secondary structures, formation of pores etc. This article
https://pubs.acs.org/doi/abs/10.1021/jp506633n suggests that hysteresis
calculation is a good indicator for hidden barriers.
In these articles (by Tse et al), convergence was assessed by the
hysteresis between upper and lower leaflet profiles.So, this should be
similar to running ABF windows by taking alternate end states as initial
Sorry for being naive
On Wed, 12 Aug 2020, 10:03 pm Chris Chipot, <chipot_at_illinois.edu> wrote:
> it is not quite clear what you refer to backward and forward PMF—ABF is
> run at thermodynamic equilibrium; it is not an out-of-equilibrium pulling
> experiment. There are many published applications out there, whereby the
> free energy was measured, using ABF, in the direction normal to a lipid
> bilayer. These free-energy calculations are usually prefaced by steered MD
> and long equilibration stages to prep the different windows along the
> permeation pathway. You may want to look at Tse et al. JCTC 2018, 2019.
> Chris Chipot
> On 8/12/20 6:13 PM, Rukhsar Ali wrote:
> I'm very new to the ABF protocol to calculate PMF. I'm wondering, if I
> want to calculate a backward PMF for a peptide insertion process into a
> bilayer, should I just pick initial structures near the lower boundary end
> state for each window and run the same simulations as in forward PMF
> calculations? I mean, for a window 10A-12A (along 'distance Z' colvar), I
> have taken the initial structure around 12A during forward PMF calculation.
> So now, for the backward PMF, should I just take the initial structure near
> Chris Chipot, Ph.D.
> CNRS research director, University of Lorraine
> Adjunct professor of physics, University of Illinois, Urbana-Champaign
> Chris Chipot, Ph.D.
> Theoretical and Computational Biophysics Group
> 3161 Beckman Institute for Advanced Science and Technology
> University of Illinois at Urbana-Champaign
> 405 North Mathews
> Urbana, Illinois 61801 Phone: (217) 244-4361
> E-mail: chipot_at_illinois.edu
> Web: https://physics.illinois.edu
> The light shines in the darkness,
> and the darkness has not overcome it
> John 1:5
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