Re: overlapping windows in ABF

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Jul 24 2018 - 22:24:52 CDT

Hi Olya, samples are combined from all files that cover an overlapping
region.

Giacomo

On Tue, Jul 24, 2018 at 7:39 PM Olya Kravchenko <ovkrav_at_gmail.com> wrote:

> Hi Jerome,
>
> thank you, this is helpful. The gradients look somewhat different in one
> of the overlapping regions, which is also less sampled, I may have to alter
> my windows.
>
> I am also trying to find out whether NAMD considers output from one file
> (say, the first listed in the merger input) or from both files for the
> overlapping region. I don't see this mentioned in any of the tutorials.
>
> Thanks a lot,
>
> Olga
>
> On Mon, Jul 23, 2018 at 5:17 PM Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>
>> Hi Olga,
>>
>> for a quick diagnosis, you could plot the free energy gradients from all
>> windows on the same graph. Overlapping regions should have similar values
>> of the gradient (keeping in mind that the gradient is always "noisier" than
>> the free energy itself, so there can be some variation). Any inconsistency
>> indicates that the two windows haven't sampled the same values of other
>> important degrees of freedom. See the literature on ABF for more info on
>> this, eg. this:
>> https://pubs.acs.org/doi/abs/10.1021/jp506633n
>>
>> Jerome
>>
>> On Mon, 23 Jul 2018 at 16:55, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>>
>>> Dear all,
>>>
>>> In my current ABF simulations two out of eight windows overlap slightly
>>> with neighboring windows, i.e. instead of 52-56, 56-60 etc. they are
>>> defined as 52-56.5, 56-60.5 (by accident).
>>>
>>> I tried both merging files as is as well as merging them after removing
>>> the overlapping portion of the data (i.e. cutting off data for 56.-56.5 and
>>> 60.-60.5) and resulting pmf plot looks different after modification.
>>>
>>> My question is, how does namd treat such overlaps? Should I concatenate
>>> overlapping windows manually without cutting off the data for overlapping
>>> 0.5A?
>>>
>>> Thanks in advance!
>>>
>>> Olga
>>>
>>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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