Re: Doubt about ABF and PMF file generation

From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Mon Nov 18 2019 - 12:52:52 CST

Thanks a lot!

On Tue, 19 Nov 2019, 00:10 Jérôme Hénin, <jerome.henin_at_ibpc.fr> wrote:

> There is no reference yet. In short, the code computes the PMF as a
> solution of a Poisson equation, which is nice because it is deterministic
> unlike the abf_integrate algorithm. The end result is the PMF whose
> numerical gradients are as close as possible (in the least squares sense)
> to the ABF estimate of the gradients.
>
> Jerome
>
> On Mon, 18 Nov 2019 at 19:27, Souvik Sinha <souvik.sinha893_at_gmail.com>
> wrote:
>
>> Great!
>>
>> So is it with NAMD 2.13?
>> And Is there any reference on how it differs from the abf_integrate
>> utility or how the multidimensional pmf is estimated?
>>
>> Thanks again for such support.
>>
>> On Mon, 18 Nov 2019, 23:48 Jérôme Hénin, <jerome.henin_at_ibpc.fr> wrote:
>>
>>> Hi Souvik,
>>>
>>> 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.
>>>
>>> Jerome
>>>
>>> On Fri, 15 Nov 2019 at 07:01, Souvik Sinha <souvik.sinha893_at_gmail.com>
>>> wrote:
>>>
>>>> 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.
>>>>
>>>> Souvik
>>>>
>>>> On Wed, Nov 13, 2019 at 4:59 AM Jérôme Hénin <jerome.henin_at_ibpc.fr>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> The PMF is significant. It is generated by solving a Poisson equation--0000000000002f318e0597a37545--

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