I encountered the same behavior with 1000 steps of ntt=0 and ntt=3 (I can't
imagine that more steps would suddenly make it better). Judging by the fact
that all of the other fields are identical, I'm going to agree with your
speculation of a computing error or else a rounding error in the printing.
On Tue, Sep 20, 2011 at 10:59 AM, Brian Radak <radak004.umn.edu> wrote:
> I haven't tried this for other thermostats yet, I'll attempt it later
> today.
>
> When I restarted the simulation with constant volume (new velocities), I
> get the same behavior again, even the first steps do not match. The
> difference is also magically always between 0.03 and 0.04, weird?
>
> Attached is a graph of the temperature distance for the beginning of the
> restart (it's still running).
>
> Brian
>
>
> On Tue, Sep 20, 2011 at 10:33 AM, David A Case <case.biomaps.rutgers.edu>wrote:
>
>> On Tue, Sep 20, 2011, Brian Radak wrote:
>>
>> > When inspecting the duplicate outputs of my TI simulations, the only
>> field
>> > that does not match exactly (differs in hundredths place) is TEMP.
>> Should I
>> > be worried?
>> >
>> > Here is the last step of 2 500ps constant pressure and temperature
>> > (Andersen) runs:
>>
>> Does this happen with other thermostats (ntt =0,1 or 3)? Does it only
>> happen
>> right at steps where new random velocities are being assigned? Since the
>> EKTOT values are the same to 8 significant figures, yet the temperatures
>> differ in the 5th signficant place, my guess is that there is a bug in
>> computing and printing the temperature.
>>
>> If you go beyond 500000 steps, do the temperatures printed on the two runs
>> come back into sync?
>>
>> ...thx...dac
>>
>> >
>> > Setting new random velocities at step 500000
>> > check COM velocity, temp: 0.012618 0.24(Removed)
>> >
>> > NSTEP = 500000 TIME(PS) = 500.000 *TEMP(K) = 307.13* PRESS
>> =
>> > 208.8
>> > Etot = -12051.3906 EKtot = 2875.8469 EPtot =
>> > -14927.2375
>> >
>> ------------------------------------------------------------------------------
>> >
>> > Setting new random velocities at step 500000
>> > check COM velocity, temp: 0.012618 0.24(Removed)
>> >
>> > NSTEP = 500000 TIME(PS) = 500.000 *TEMP(K) = 307.16* PRESS
>> =
>> > 208.8
>> > Etot = -12051.3906 EKtot = 2875.8469 EPtot =
>> > -14927.2375
>>
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>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Wright-Rieman Hall 101
> Graduate Program in Chemical Physics : 610 Taylor Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
> radak004.umn.edu :
> radakb.biomaps.rutgers.edu
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
>
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Wright-Rieman Hall 101
Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Tue Sep 20 2011 - 11:30:04 PDT
