Hi Jason,
thanks for the explanation but to be frank I did not understand the main
idea.
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 ?
Thanks,
Marek
Dne Wed, 29 May 2013 22:44:18 +0200 Jason Swails <jason.swails.gmail.com>
napsal/-a:
> 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.
>
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Received on Wed May 29 2013 - 15:30:03 PDT
