ok
Maybe someone can comment, but the amber cpu code is NOT bit-wise
reversible, so different runs will give you different answers if you run
then long enough.
The cuda code MUST give you the EXACT same answers. If not, then your
card is broken.
For CPUS, you must look at simple averages to see if your simulations
are different or not, not at the individual steps. Plot for instance a
distribution of a variable, such as radius of gyration. If the two
simulations give you statistically different distribution, then neither
of them is 'converged'.
Adrian
On 6/5/17 11:28 PM, pengfei li wrote:
> Hi Adrian,
>
> Thanks for your quick reply.
>
>> On Jun 5, 2017, at 9:24 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
>>
>> Hi
>>
>> Not sure what you mean.
>>
>> Same random seed and same coordinates/prmtop, etc ?
>>
> Yes, both the random seed and coordinates/prmtop are the same. The simulations are 500 ps long each.
>
>> What do you mean by different results ?
>>
> The output files are different (numbers could not match), and final restart files are different.
>
>> Was this amber gpu or what ?
> It was pemed.MPI. Both used 16 cpus.
>
> Best regards,
> Pengfei
>
>> Tell us the details please.
>>
>> adrian
>>
>>
>> On 6/5/17 11:22 PM, pengfei li wrote:
>>> Hi everyone,
>>>
>>> I have performed two simulations with the same random seed but got different results. Except the random seed, what are the other factors that influence the reproducibility of the MD simulation? Thanks!
>>>
>>> Best regards,
>>> Pengfei
>>> _______________________________________________
>>> AMBER-Developers mailing list
>>> AMBER-Developers.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>> --
>> Dr. Adrian E. Roitberg
>> University of Florida Research Foundation Professor
>> Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>> 352-392-6972
>>
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Mon Jun 05 2017 - 08:00:03 PDT
