Re: Doubt about ABF and PMF file generation

From: Souvik Sinha (
Date: Fri Nov 15 2019 - 00:03:11 CST

Sorry, if I'm missing something here. As far as I know, for 2D or greater,
*abf_integate* is the only available utility to reconstruct the landscape.
Is there any update on that? I checked the NAMD 2.13 user guide, but
couldn't find anything else than *abf_integrate * to build a 2D PMF.


On Wed, Nov 13, 2019 at 4:59 AM Jérôme Hénin <> wrote:

> Hi,
> The PMF is significant. It is generated by solving a Poisson equation. It
> is optimal in the sense that its numerical gradient is as close as possible
> to the ABF gradients, given the boundary conditions. It's better than that
> generated by the abf_integrate tool because the algorithm is deterministic,
> and its convergence is much better behaved.
> Jerome
> On Mon, 11 Nov 2019 at 21:20, Ercalary . <> wrote:
>> Dear NAMD community, I have the following doubt about the pmf generation
>> when I apply abf in two dimensions. Is the PMF that is generated meaningful
>> or I should work only with the gradient file instead?
>> Beforehand thank you very much!

Souvik Sinha
Research Fellow
Division of Bioinformatics
Bose Institute, Kolkata
Contact: 033 25693275

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