**From:** Abhishek Acharya (*abhi117acharya_at_gmail.com*)

**Date:** Thu Nov 19 2020 - 00:02:49 CST

**Next message:**Francesco Pietra: "Restarting QMMM"**Previous message:**Jérôme Hénin: "Re: performing SMD in Z using colvar module"**In reply to:**Jérôme Hénin: "Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator."**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dear Jerome,

I had performed some initial test runs for about 25 ns per walker. The

artefacts were observed in both .pmf and .czar.pmf files.

Yes I am writing the zgrad files that I hope to use for constructing the

final pmf.

Thank you very much for your help.

Abhishek

On Mon, Nov 16, 2020 at 9:10 PM Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

*> Hi Abhishek,
*

*>
*

*>
*

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

*> wrote:
*

*>
*

*> > Hello Jerome,
*

*> >
*

*> > Thank you for your quick response.
*

*> >
*

*> > Well it does look simpler that I thought. Pardon my ignorance; I am a
*

*> > biologist by training, so mathematics is not a strong suit (how I wish it
*

*> > was).
*

*> >
*

*> > 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
*

*> > combine all of these to obtain the full joint histogram, calculate the
*

*> > marginal and use the final full 1D PMF to obtain the 2D distribution.
*

*> But I
*

*> > am concerned that sampling artefacts at the window edges may cause
*

*> > problems.
*

*>
*

*> 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
*

*> > window, drop the values at the edges and perform an interpolation to
*

*> obtain
*

*> > the complete 2D PMF.
*

*> > 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.
*

*> > This would be slightly expensive but perhaps a bit cleaner.
*

*>
*

*> Yes, overlapping windows always work as well.
*

*>
*

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

*>
*

*> Cheers
*

*> Jerome
*

*>
*

*>
*

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

*> wrote:
*

*> >
*

*> >> Hello Abhishek,
*

*> >>
*

*> >> you're almost there, but it's simpler than you think. If you can collect
*

*> >> the joint histogram P(z1, z2), biased along z1, then you can obtain the
*

*> 2d
*

*> >> PMF by reweighting using the 1d CZAR PMF:
*

*> >> A(z1, z2) = -kT ln( P(z1, z2) / P(z1) ) + A_CZAR(z1)
*

*> >>
*

*> >> where P(z1) is the observed (biased) histogram in z1 (aka the z1
*

*> marginal
*

*> >> of the 2d histogram).
*

*> >>
*

*> >> Best,
*

*> >> Jerome
*

*> >>
*

*> >>
*

*> >> ----- On 11 Nov 20, at 20:04, Abhishek Acharya abhi117acharya_at_gmail.com
*

*> >> wrote:
*

*> >>
*

*> >> > Hello,
*

*> >> >
*

*> >> > 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.
*

*> >> >
*

*> >> > Obtaining the 1D PMF looks straightforward to do. Just to be sure we,
*

*> >> > 1) Combine data for walkers using the inputPrefix directive of ABF to
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*> get
*

*> >> > combined outputs for each window.
*

*> >> > 2) Combine the gradients for each window to obtain the full gradient,
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*> >> > taking care of the edge values.
*

*> >> > 3) Integrate the gradient to obtain 1D PMF.
*

*> >> >
*

*> >> > However for better insights and comparison with methods used
*

*> previously,
*

*> >> we
*

*> >> > would like to obtain a PMF projected along an additional CV to obtain
*

*> a
*

*> >> 2D
*

*> >> > picture. So, the idea is to apply ABF bias along, say z1 CV, but also
*

*> >> > obtain samples along z2 (unbiased and defined without the Extended
*

*> >> > Largrangian directive) and somehow combine these to obtain the 2D PMF.
*

*> >> > Naively, I thought that maybe we can do a post-hoc estimation using
*

*> the
*

*> >> > CZAR estimator; essentially obtain the biased 2D histogram, P(z1, z2)
*

*> and
*

*> >> > the z1-averaged forces from the CV values and total forces printed
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*> out to
*

*> >> > the colvar traj file, and finally using the 1D CZAR expression to
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*> obtain
*

*> >> > the 2D PMF.
*

*> >> >
*

*> >> > 1. Is this at all a correct strategy? If not, some hints would be
*

*> >> helpful.
*

*> >> >
*

*> >> > 2. Fu et al, *J. Chem. Theory Comput.* 2016 indicates that accurate
*

*> >> > post-hoc analysis would require printing out the CV and force values
*

*> >> every
*

*> >> > timestep. For the aforesaid procedure, I thought that maybe we can use
*

*> >> the
*

*> >> > histogram directive to obtain the final 2D counts and combine it with
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*> the
*

*> >> > 1D averaged forces.
*

*> >> >
*

*> >> > Any suggestions would be highly appreciated.
*

*> >> >
*

*> >> > Thanks in advance.
*

*> >> >
*

*> >> > Sincerely,
*

*> >> > Abhishek Acharya
*

*>
*

**Next message:**Francesco Pietra: "Restarting QMMM"**Previous message:**Jérôme Hénin: "Re: performing SMD in Z using colvar module"**In reply to:**Jérôme Hénin: "Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator."**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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