From: Pedro Swagger (pedrito.swagger_at_gmail.com)
Date: Wed Jul 10 2013 - 16:45:15 CDT
By the way, I run first a SMD simulation and I am dividing that simulation
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)?
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.
>> Pedro Swagger
>> 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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