Hi Brian,
Which version of sander did you use (did you download from the
repository)? If you won't mind providing me with your input files,
I'll try and see if I can reproduce the problem?
Thanks,
Qiantao
On Tue, Sep 20, 2011 at 2:23 PM, Brian Radak <radak004.umn.edu> wrote:
> 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.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Sep 20 2011 - 13:00:02 PDT
