Thank you Professor Adrian for your reply.
On Mon, Oct 8, 2012 at 2:40 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> Soumya.
>
> The issue you raise in very interesting.The easy answer is that you
> cannot scale the time step. This is because you use a 'real' time step
> in a modified potential energy surface (amd surface) and that cannot be
> easily related to a change in 'time'.
>
> If you run long enough, you can see how long it takes to jump over
> barriers with regular md and amd, and that should scale trivially with
> barrier height. That gives you a scaled time scale. However, the scaling
> factor depends very much on your position in the surface. Your minima
> are higher in energy in AMD, but the barriers do not change (in absolute
> energy). So, you do not have a global scaling factor.
>
> As a recipe, unless you can really validate things, you should NOT use
> amd to derive time scales for processes. Just stick with the
> thermodynamics of the problem and you are safe.
>
> Adrian
>
>
> On 10/8/12 10:25 AM, Romelia Salomon wrote:
> > Dear Soumya
> >
> > The amd.log file contains the AMD pertinent information produced along
> the
> > calculation. It is printed every time the trajectory is printed, as those
> > are the configuration points that will be available for analysis.
> >
> > The information being printed is:
> >
> > 1) The total potential energy for that step (without the extra added by
> > AMD, to keep in reference with mdout)
> > 2) the total dihedral energy for that step (without the extra added by
> > AMD, to keep in reference with mdout)
> > 3) factor by which total forces are scaled
> > 4) factor by which dihedral forces are scaled
> > 5) energy added by AMD to the total potential energy
> > 6) energy added by AMD to the dihedral energies
> >
> > I hope this helps.
> >
> > Romelia
> >
> >
> >> Dear Amber Users,
> >>
> >> I wanted to calculate the modified time step Ät* in the accelerated MD
> >> which one can find by using the equation Ät x boost factor. How can one
> >> get
> >> the value for boost factor?
> >>
> >> Thanks
> >>
> >> Soumya
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
> --
> Dr. Adrian E. Roitberg
> Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
> roitberg.ufl.edu
>
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Received on Mon Oct 08 2012 - 07:30:02 PDT
