Re: Differences between z-gradient and gradient in ABF simulation

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Nov 04 2019 - 07:12:57 CST

Dear Surbhi,

The theory is developed in this article:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5402294/

One point of your question that is not discussed explicitly there is the
question of stratified simulations. That's explained briefly in the doc
(which you've seen, but here is the link for the record:
http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvarbias_ti_ext_czar)
If you haven't run a trajectory in the complete space, then you can just
concatenate the CZAR estimates of the gradients in each window to get the
final free energy for the full range.

Best,
Jerome

On Mon, 28 Oct 2019 at 12:26, Surbhi patel <psurbhi920_at_gmail.com> wrote:

> Dear NAMD community,
>
>
>
> I would like to know the differences between z-gradient and gradient in
> ABF simulation.
>
>
>
> Why is it better to use the z-gradient when a stratified eABF simulation
> is performed? And also, what is the best way to merge the windows?
>
>
>
> Thanks!
>
> Surbhi
>

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