**From:** Jérôme Hénin (*jerome.henin_at_ibpc.fr*)

**Date:** Mon Nov 16 2020 - 14:10:50 CST

**Next message:**Ropón-Palacios G.: "performing SMD in Z using colvar module"**Previous message:**Francesco Pietra: "Re: Setting up QM-MM with homotrimer"**In reply to:**Abhishek Acharya: "Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator."**Next in thread:**Abhishek Acharya: "Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator."**Reply:**Abhishek Acharya: "Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator."**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi Abhishek,

----- On 11 Nov 20, at 23:13, Abhishek Acharya abhi117acharya_at_gmail.com wrote:

*> Hello Jerome,
*

*>
*

*> Thank you for your quick response.
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*>
*

*> Well it does look simpler that I thought. Pardon my ignorance; I am a
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*> biologist by training, so mathematics is not a strong suit (how I wish it
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*> was).
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*>
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*> I have another follow up question. Looks like I can collect the joint
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*> histogram for all the walkers using the histogram method. Easiest way is to
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*> combine all of these to obtain the full joint histogram, calculate the
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*> marginal and use the final full 1D PMF to obtain the 2D distribution. But I
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*> am concerned that sampling artefacts at the window edges may cause
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*> problems.
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Do you see artefacts in both the "regular" PMF and CZAR PMF?

*> A better way would be to calculate the 2D PMF separately for each
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*> window, drop the values at the edges and perform an interpolation to obtain
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*> the complete 2D PMF.
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*> A third way I thought is to define slightly broader (and overlapping)
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*> window ranges. This way I can simply combine the data across windows (for
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*> both 1D and 2D cases) after dropping the problematic bins at both ends.
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*> This would be slightly expensive but perhaps a bit cleaner.
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Yes, overlapping windows always work as well.

At any rate, you are going to need the writeCZARwindowFile at some point to combine the windows.

Cheers

Jerome

*> On Wed, Nov 11, 2020 at 8:53 PM Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
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*>
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*>> Hello Abhishek,
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*>>
*

*>> you're almost there, but it's simpler than you think. If you can collect
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*>> the joint histogram P(z1, z2), biased along z1, then you can obtain the 2d
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*>> PMF by reweighting using the 1d CZAR PMF:
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*>> A(z1, z2) = -kT ln( P(z1, z2) / P(z1) ) + A_CZAR(z1)
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*>>
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*>> where P(z1) is the observed (biased) histogram in z1 (aka the z1 marginal
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*>> of the 2d histogram).
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*>>
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*>> Best,
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*>> Jerome
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*>>
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*>>
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*>> ----- On 11 Nov 20, at 20:04, Abhishek Acharya abhi117acharya_at_gmail.com
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*>> wrote:
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*>>
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*>> > Hello,
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*>> >
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*>> > We are trying to run 1D eABF simulations on our system of interest.
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*>> > Specifically, the simulation is divided into 3 windows and we use 5
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*>> walkers
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*>> > per window for sampling.
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*>> >
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*>> > Obtaining the 1D PMF looks straightforward to do. Just to be sure we,
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*>> > 1) Combine data for walkers using the inputPrefix directive of ABF to get
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*>> > combined outputs for each window.
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*>> > 2) Combine the gradients for each window to obtain the full gradient,
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*>> > taking care of the edge values.
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*>> > 3) Integrate the gradient to obtain 1D PMF.
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*>> >
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*>> > However for better insights and comparison with methods used previously,
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*>> we
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*>> > would like to obtain a PMF projected along an additional CV to obtain a
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*>> 2D
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*>> > picture. So, the idea is to apply ABF bias along, say z1 CV, but also
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*>> > obtain samples along z2 (unbiased and defined without the Extended
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*>> > Largrangian directive) and somehow combine these to obtain the 2D PMF.
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*>> > Naively, I thought that maybe we can do a post-hoc estimation using the
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*>> > CZAR estimator; essentially obtain the biased 2D histogram, P(z1, z2) and
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*>> > the z1-averaged forces from the CV values and total forces printed out to
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*>> > the colvar traj file, and finally using the 1D CZAR expression to obtain
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*>> > the 2D PMF.
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*>> >
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*>> > 1. Is this at all a correct strategy? If not, some hints would be
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*>> helpful.
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*>> >
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*>> > 2. Fu et al, *J. Chem. Theory Comput.* 2016 indicates that accurate
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*>> > post-hoc analysis would require printing out the CV and force values
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*>> every
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*>> > timestep. For the aforesaid procedure, I thought that maybe we can use
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*>> the
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*>> > histogram directive to obtain the final 2D counts and combine it with the
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*>> > 1D averaged forces.
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*>> >
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*>> > Any suggestions would be highly appreciated.
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*>> >
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*>> > Thanks in advance.
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*>> >
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*>> > Sincerely,
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*>> > Abhishek Acharya
*

**Next message:**Ropón-Palacios G.: "performing SMD in Z using colvar module"**Previous message:**Francesco Pietra: "Re: Setting up QM-MM with homotrimer"**In reply to:**Abhishek Acharya: "Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator."**Next in thread:**Abhishek Acharya: "Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator."**Reply:**Abhishek Acharya: "Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator."**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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