On Mar 23, 2013, at 5:51 PM, George Tzotzos <gtzotzos.me.com> wrote:
> In the manual for Amber 11p.108 it is stated that
> The method should be thought of as an umbrella sampling where the center of the restraint is time-dependent as in:
>
> Vrest (t) = (1/2)k[x − x0(t)]2
>
> where x could be a distance, an angle, or a torsion between atoms or groups of atoms.
>
> My question is how does the above equation define the centre of the restraint?
The 'center' of the restraint is the value at which the restraint potential is zero (i.e., x0). Think about it as the center of the quadratic restraint potential.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Mar 23 2013 - 19:30:02 PDT
