From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Mon Nov 18 2019 - 12:26:33 CST
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.
>>> 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 . <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
>>
>
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:12 CST