Re: ABF subdividing the reaction coordinate

From: Aron Broom (
Date: Wed Jul 10 2013 - 16:22:28 CDT

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 <>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

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