Re: ABF in various simulations

From: stefhoor (fabracht1_at_gmail.com)
Date: Mon May 17 2010 - 11:31:03 CDT

Could you please specify this link. I looked it up on namd's web site and
didn't find it.
Thank you

2010/5/17 Patrick Yee <pyee_at_nd.edu>

> 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 <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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