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

**Date:** Wed Nov 11 2020 - 13:04:29 CST

**Next message:**Jérôme Hénin: "Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator."**Previous message:**Ropón-Palacios G.: "Re: FEP/λ-REMD Simulation error"**Next in thread:**Jérôme Hénin: "Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator."**Reply:**Jérôme Hénin: "Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator."**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hello,

We are trying to run 1D eABF simulations on our system of interest.

Specifically, the simulation is divided into 3 windows and we use 5 walkers

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 get

combined outputs for each window.

2) Combine the gradients for each window to obtain the full gradient,

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 out to

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

1D averaged forces.

Any suggestions would be highly appreciated.

Thanks in advance.

Sincerely,

Abhishek Acharya

**Next message:**Jérôme Hénin: "Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator."**Previous message:**Ropón-Palacios G.: "Re: FEP/λ-REMD Simulation error"**Next in thread:**Jérôme Hénin: "Re: Calculating 2D PMF from 1D eABF simulations using CZAR estimator."**Reply:**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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