Re: ABF subdividing the reaction coordinate

From: Pedro Swagger (pedrito.swagger_at_gmail.com)
Date: Wed Jul 10 2013 - 17:15:44 CDT

Yes, I have the complete SMD trajectory. I don't know if I am
understanding well, but you mean after I dividing my SMD simulation into
windows for ABF, I can take any configuration of my system inside each
window for starting the ABF simulation for each respective window, and
after merging all of them together I should similar results as I do the ABF
from the begining without using windows. Am I right?

And last question why do we use that approach of using windows from SMD?
Why no to do ABF without windows?

I got the approach for using windows from the tutorial entitled "Forcing
substrates through channels" but I am not getting the real meaning of doing
that.

Sorry for many question.

Thanks again.

On Wed, Jul 10, 2013 at 6:01 PM, Aron Broom <broomsday_at_gmail.com> wrote:

> So you're taking the trajectory from SMD and using points along that as
> the starting points for your ABF? That sounds like a reasonable way to
> proceed. Assuming your ABF converges fully, the results should be the same
> as using any other starting point for the windows (again assuming
> convergence).
>
>
> On Wed, Jul 10, 2013 at 5:45 PM, Pedro Swagger <pedrito.swagger_at_gmail.com>wrote:
>
>> Thanks Aron,
>>
>> By the way, I run first a SMD simulation and I am dividing that
>> simulation in windows.
>>
>> I have another question. Since I am taking the reference points of the
>> system from a previous SMD for each starting windows, would the results be
>> similar to if I run my system from the beginning using only ABF with
>> windows (point of reference)?
>>
>> Thanks again
>>
>>
>>
>>
>>
>> On Wed, Jul 10, 2013 at 5:22 PM, Aron Broom <broomsday_at_gmail.com> wrote:
>>
>>> If you are going to start a new simulation or "window" you can
>>> reasonably take any snapshot from the previous window, but ideally you
>>> would take one in which the reaction coordinate is closest to the new
>>> window. Better yet, since you probably want reasonable overlap between
>>> adjacent windows, you can take a snapshot from the previous window in which
>>> the reaction coordinate is actually in the next windows range.
>>>
>>>
>>> On Wed, Jul 10, 2013 at 5:00 PM, Pedro Swagger <
>>> pedrito.swagger_at_gmail.com> wrote:
>>>
>>>> Dear everybody,
>>>>
>>>> I am trying to use ABF and I have some questions. It may be a garbage
>>>> questions, but I am new to this. Sorry and apologize me.
>>>>
>>>> When subdividing the reaction coordinate in equally spaced window for
>>>> your ABF simulation, the starting point for the simulation (in each new
>>>> window) should be the begining configuration of the protein in that window?
>>>> or it could be any configuration inside the window.
>>>>
>>>>
>>>> Thanks
>>>> --
>>>> Pedro Swagger
>>>>
>>>> Saludos
>>>>
>>>> Departamento de Física,
>>>> Facultad de Ciencias,
>>>>
>>>> Universidad de Chile
>>>> Las Palmeras 3425, Ñuñoa, Santiago, Chile
>>>>
>>>
>>>
>>>
>>> --
>>> Aron Broom M.Sc
>>> PhD Student
>>> Department of Chemistry
>>> University of Waterloo
>>>
>>
>>
>>
>> --
>> Pedro
>>
>>
>> Saludos
>>
>> Departamento de Física,
>> Facultad de Ciencias,
>>
>> Universidad de Chile
>> Las Palmeras 3425, Ñuñoa, Santiago, Chile
>>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>

-- 
Pedro
Saludos
Departamento de Física,
Facultad de Ciencias,
Universidad de Chile
Las Palmeras 3425, Ñuñoa, Santiago, Chile

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