Yes I think you've got it all under control :)
~Aron
On Mon, Nov 5, 2012 at 9:06 AM, Sajeewa Pemasinghe <sajeewasp.gmail.com>wrote:
> Thank you very much Dr. Steinbrecher. It was really helpful.
>
> Sajeewa Dewage
>
> On Mon, Nov 5, 2012 at 3:20 AM, <steinbrt.rci.rutgers.edu> wrote:
>
> > Hi,
> >
> > > I was specifically asking in the second part of my question was "from
> > > where
> > > to where is r1 measured?" AND "from where to where is r4 measured?"
> >
> > Both of them are measured as distance d between the two atoms/groups. The
> > range d=0...r1 has a linear potential shape, d=r1...r2 is a harmonic
> > potential, d=r2...r3 no restraint, r3...r4 harmonic again and
> > r4...\infinity a linear potential. If you want a harmonic potential at
> rx,
> > then you would set
> >
> > r1=0
> > r2=rx
> > r3=rx
> > r4=99999 (or something else bigger than your box)
> >
> > At least that's how it was when I last used Amber US.
> >
> > Oner more thing, there is nothing in US that specifically requires a
> > harmonic potential. Any shape at all could be used, it is only that many
> > analysis programs (like e.g. wham) typically assume a harmonic potential
> > shape. So depending on how you want to calculate the final free energies,
> > you may even be able to use Amber's more complex potentials, but in most
> > cases it will be simpler to just use harmonic potentials.
> >
> > Kind Regards,
> >
> > Thomas
> >
> > Dr. Thomas Steinbrecher
> > formerly at the
> > BioMaps Institute
> > Rutgers University
> > 610 Taylor Rd.
> > Piscataway, NJ 08854
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Mon Nov 05 2012 - 09:00:04 PST
