Re: ABF subdividing the reaction coordinate

From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Jul 10 2013 - 17:01:01 CDT

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

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