Re: ABF in various simulations

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Mon May 17 2010 - 11:08:28 CDT

Hi,

What you are doing, splitting the pathway into windows, is correct. In
addition, you can run the calculation for each window in a series of
shorter runs, simply by restarting each run from NAMD's restart files,
and specifying the colvarsInput keyword (see user's guide for
details).

Jerome

On 17 May 2010 15:30, stefhoor <fabracht1_at_gmail.com> 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 Distance.in files (Distance.in being the files with parameters for
> the ABF).
> Each of the Distance.in 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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