From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Nov 18 2019 - 12:18:14 CST
Colvars now includes a facility to integrate PMFs in 2d and 3d. The user
guide needs to be updated, that's on my TODO list. If you don't do
anything, the PMFs will be calculated by default.
On Fri, 15 Nov 2019 at 07:01, Souvik Sinha <souvik.sinha893_at_gmail.com>
> 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 <jerome.henin_at_ibpc.fr> wrote:
>> 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.
>> On Mon, 11 Nov 2019 at 21:20, Ercalary . <ercalary20_at_gmail.com> 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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