Hi,
Thank you all for your answers.
Regards,
Manasa.
On Fri, Aug 28, 2026 at 6:55 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> The best explanation for this is in the Amber manual in "31.1.
> Distance, angle and torsional restraints":
>
> • R < r1 Linear, with the slope of the "left-hand" parabola at the point
> R=r1.
> • r1 <= R < r2 Parabolic, with restraint energy k2(R−r2)^2
> • r2 <= R < r3 E = 0.
> • r3 <= R < r4 Parabolic, with restraint energy k3(R−r3)^2
> • r4 <= R Linear, with the slope of the "right-hand" parabola at the point
> R=r4
>
> So if the current distance between the two atoms R is between r1 and
> r2 the restraint function is k2 * (R-r2)^2.
>
> Hope this helps,
>
> -Dan
>
> On Tue, Aug 25, 2026 at 4:15 PM Manasa Bharath ic44158 via AMBER
> <amber.ambermd.org> wrote:
> >
> > Dear AMBER developers,
> >
> > I have a question about the &rst distance restraint in AMBER.
> >
> > For a constant-force setup, if r1 and r2 are separated by a small
> distance,
> > does r2-r1 represent the maximum distance the restrained atoms or
> molecule
> > can stretch or the limit when force should act? Is there a computational
> or
> > mathematical logic behind this? If yes, please explain that.
> >
> > Regards,
> >
> > Manasa
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Aug 31 2026 - 21:30:05 PDT
