Hi Brian,
> Just going from my gut here but I think you might expect that kind of
> behavior for any set of 3 atoms, although it probably depends on how you
> are defining the instantaneous temperature (how are you
> defining/calculating it?).
Fabricios gut feeling is correct, the temperature for a small number of
atoms is no longer well defined. Since it is merely computed from the
average of the kinetic energies, which change rapidly, you will see large
fluctuations, up to >100K for one atom. In the extreme case of one bonded
atom in vacuum, you would see a 'temperature' for the oscillator equal to
a sine wave. So this behaviour is normal and nothing to worry. At the end
of the simulation, your average simulation temperature should be close to
the thermostate one.
Thomas
> On Tue, Oct 16, 2012 at 2:49 PM, Fabrício Bracht <bracht.iq.ufrj.br>
> wrote:
>
>> Is it normal for the temperature to oscillate substantially in the
>> soft core region. I got these outputs from the mdout file of a TI run
>>
>> Softcore part of the system: 3 atoms, TEMP(K) =
>> 660.04
>>
>> And for the next output...
>>
>> Softcore part of the system: 3 atoms, TEMP(K) =
>> 43.50
>>
>> I have set for the temperature of the system to be 298 K ntt = 3 and
>> gamma_ln = 1
>>
>> The system temperature seems to be in order, it oscillates around 298 K.
>>
>> Thank you
>> Fabrício
>>
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>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
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Dr. Thomas Steinbrecher
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Rutgers University
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Received on Wed Oct 17 2012 - 01:00:02 PDT
