Re: ABF in various simulations

From: Patrick Yee (
Date: Mon May 17 2010 - 10:47:58 CDT

Yes, this is a normal approach so long as the "windows" are not
overlapping. See the tutorial files on the ABF website (there is a
link on the NAMD website) for basic information on concatenating PMFs
from ABF simulations

On 5/17/10, stefhoor <> wrote:
> I need to calculate the free energy of dimerization using ABF. The problem
> is that the cluster rules here allow me only to run 24Hs maximum simulation
> time. So, what I usually do is to separate my simulations into several
> different subsimulations and in the and concatenate all the files I need to
> analyse. Would that be possible with ABF.
> I have tried doing so by writing 5 different parameters.conf files and 5
> different files ( being the files with parameters for
> the ABF).
> Each of the files covers a part of the lower and upper distance
> to monitor,i.e., the first file contains the lines
> lowerboundary 2.0
> upperboundary 7.6
> the second file
> upperboundary 7.6
> upperboundary 13.2
> and so on and so forth.
> Is that a correct approach? Or am I doing something wrong?
> Thank you

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