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 - 00:30:02 PST
