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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Received on Mon Nov 05 2012 - 06:30:03 PST
