On Wed, May 29, 2013 at 6:00 PM, Marek Maly <marek.maly.ujep.cz> wrote:
> Hi Jason,
>
> thanks for the explanation but to be frank I did not understand the main
> idea.
>
I'll try to explain a little bit (but perhaps it's better to just take
Scott's advice and trust him on that). The problem is that addition of
floating point numbers in computers is not strictly associative. That is,
a + (b + c) != (a + b) + c, due to round-off issues in the last decimal
place or so. As a result, the numerical result of a summation on a
computer depends on the _order_ in which those numbers are added. If you
change the 'order of operations,' then you risk changing the exact value of
the result in the last stored decimal. See the wikipedia page on Floating
point accuracy:
https://en.wikipedia.org/wiki/Floating_point#Accuracy_problems
Since the force calculation and energy calculation follow different code
paths, the 'order of operations' differs between the two routines. As a
result, the exact forces may vary a tinytinytiny bit depending on whether
the force or energy routine was called. This difference is tiny and
negligible, but since classical systems of <2 bodies are chaotic these
differences eventually manifest as completely different trajectories.
As Scott said, this difference is expected, unavoidable, and conveniently
unimportant. (In fact, some may argue it's a _good thing_).
>
> I understand that for system evolution by Molecular Dynamics is not
> necessary to calculate energy
> just forces and so that energy is calculated only when explicitly
> requested (i.e. with NTPR step period) but what I have problem to
> understand is why the printed (in mdout file) immediate energy value E(i)
> at step "i" should be dependent on the number of my "Energy requests"
> before the simulation reached step "i" (i.e. dependent on NTPR value)? I
> naturally assume that my energy requests do not influence evolution of my
> molecular system by Molecular Dynamics (e.g. do not influence forces ...).
> I see NTPR parameter just as the period in which some function
> "CALCULATE_ENERGIES" is called to calculate all the energy components of
> the simulated system in given moment, that's all, but perhaps I am not
> right here ?
>
> How exactly "ene_avg_sampling" parameter is connected with "NTPR"
> parameter ?
>
Like the "ntpr" parameter, the ene_avg_sampling variable tells pmemd how
frequently you _want_ it to calculate energies. If ene_avg_sampling is set
to 10, then pmemd.cuda will compute energies every 10 steps so they can be
averaged. If ntpr is any multiple of 10, then pmemd.cuda will still
compute energies _only_ every 10 steps (so that it can be averaged that
often). As a result, the code path is dictated by the fact that
ene_avg_sampling is 10 rather than by the value of ntpr.
I hope this clarified things a little bit...
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed May 29 2013 - 20:00:02 PDT
