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

**Date:** Mon Jan 29 2018 - 11:13:55 CST

**Next message:**Brian Radak: "Re: Question on restraint behavior when part of system decouples"**Previous message:**Giacomo Fiorin: "Re: Calculation of Diffusion coefficient"**In reply to:**Giacomo Fiorin: "Re: Calculation of Diffusion coefficient"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Thanks, I will work on it.

On 29 Jan 2018 10:14 p.m., "Giacomo Fiorin" <giacomo.fiorin_at_gmail.com>

wrote:

*>
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*>
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*> On Mon, Jan 29, 2018 at 11:35 AM, Souvik Sinha <souvik.sinha893_at_gmail.com>
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*> wrote:
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*>
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*>> Okay, I get that calculating diffusion coefficient may not be of much use
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*>> in this context.
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*>>
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*>> Sorry, I didn't get what you meant by this: "How about you simply take
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*>> the last part of the ABF simulation, where the biasing force doesn't change
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*>> much due to convergence, and you assume a net total force of zero on the
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*>> variable? "
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*>>
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*>
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*> That's for estimating the diffusion coefficient.
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*>
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*>
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*>>
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*>> If the PMF is converged, then certainly the net total force would be zero
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*>> on my specified variable. Sorry, I didn't check the convergence till now
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*>> which I can definitely do by plotting the PMF at the different time point
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*>> and see whether it is converged or not.
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*>>
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*>
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*> I'd recommend doing that: permeation of a whole peptide across a bilayer
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*> is a difficult computation.
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*>
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*>
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*>> But if I wanna check the uncertainty of the calculated PMF, I need to
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*>> have the system force trajectory file for the calculation of say, mean
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*>> autocorrelation of force at the different regime of the RC [ J. Phys.
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*>> Chem. B, 2015, 119 (3), pp 1129–1151 ]. So, is there any way I can get
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*>> that now without re-running all the windows?
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*>>
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*>
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*> For estimating the uncertainty of the PMF (unrelated to the diffusion
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*> coefficient), try recomputing forces, Colvars and ABF on the existing DCD
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*> files through "coorfile" and "run 0". If the result is not acceptable to
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*> you, you may have to run additional trajectories, starting from the latest
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*> restarts.
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*>
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*> Giacomo
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*>
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*>
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*>>
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*>> Please excuse me being naive about all the intricacies.
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*>>
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*>> Thanks for your quick response.
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*>>
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*>> On Mon, Jan 29, 2018 at 9:32 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com
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*>> > wrote:
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*>>
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*>>> Hi Souvik, FYI you may also want to take a look at the more recent
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*>>> papers by Jeff Comer regarding computing permeabilities of small molecules
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*>>> across a bilayer.
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*>>>
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*>>> For something larger, like a peptide, you are definitely much more bound
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*>>> by the PMF than by the differences in diffusion coefficient. This may be
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*>>> less of a problem for you, because the diffusion coefficient changes by
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*>>> less than an order of magnitude between lipid bilayers and bulk water.
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*>>>
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*>>> As for recomputing the system force along the trajectory, you do have
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*>>> its average already computed along the collective variable, given by the
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*>>> PMF (is it converged?). Computing the system force as a function of time
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*>>> would only help you in collecting diffusion data during the transient
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*>>> regime before convergence. Re-running on the single-precision, sparsely
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*>>> collected trajectories may not be of much help.
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*>>>
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*>>> How about you simply take the last part of the ABF simulation, where the
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*>>> biasing force doesn't change much due to convergence, and you assume a net
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*>>> total force of zero on the variable?
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*>>>
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*>>> Giacomo
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*>>>
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*>>>
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*>>>
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*>>> On Mon, Jan 29, 2018 at 9:01 AM, Souvik Sinha <souvik.sinha893_at_gmail.com
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*>>> > wrote:
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*>>>
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*>>>> Hi,
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*>>>>
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*>>>> Currently, I am estimating a peptide insertion (into membrane) free
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*>>>> energy profile using ABF. I want to calculate the local diffusion
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*>>>> coefficient along the reaction coordinate for which I need the estimation
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*>>>> of 'time autocorrelation function of the fluctuations of the instantaneous
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*>>>> forces' *[ J. Phys. Chem. B, 2011, 115 (49), pp 14704–14712 ]*--001a11458c320fb78f0563ed5f1e--
*

**Next message:**Brian Radak: "Re: Question on restraint behavior when part of system decouples"**Previous message:**Giacomo Fiorin: "Re: Calculation of Diffusion coefficient"**In reply to:**Giacomo Fiorin: "Re: Calculation of Diffusion coefficient"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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