I'll answer a little bit:
NTPR=10 Etot after 2000 steps
>
> -443256.6711
> -443256.6711
>
> NTPR=200 Etot after 2000 steps
>
> -443261.0705
> -443261.0705
>
> Any idea why energies should depend on frequency of energy records (NTPR) ?
>
It is a subtle point, but the answer is 'different code paths.' In
general, it is NEVER necessary to compute the actual energy of a molecule
during the course of standard molecular dynamics (by analogy, it is NEVER
necessary to compute atomic forces during the course of random Monte Carlo
sampling).
For performance's sake, then, pmemd.cuda computes only the force when
energies are not requested, leading to a different order of operations for
those runs. This difference ultimately causes divergence.
To test this, try setting the variable ene_avg_sampling=10 in the &cntrl
section. This will force pmemd.cuda to compute energies every 10 steps
(for energy averaging), which will in turn make the followed code path
identical for any multiple-of-10 value of ntpr.
--
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 - 14:00:04 PDT
