ok
thank you very much sir
mary varughese
On 7/16/14, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Jul 15, 2014 at 6:57 PM, Mary Varughese <maryvj1985.gmail.com>
> wrote:
>
>> sir,
>>
>> above mentioned topic link:
>> http://archive.ambermd.org/201207/0098.html
>>
>> you have said ; if you are using NTT=3 the random
>> number generator on the CPU is different from that used on the 3 GPU runs
>> which would account for the differences in such short runs.
>>
>> i also used ntt=3 ; i feel there is much difference in my 15 ns cpu and
>> gpu
>> runs. That's why i asked ; which valid ntt value could be used which have
>> no such problem.
>>
>
> The problem is not your thermostat. The problem is that you expect your
> results to converge within 15 ns.
>
> Even running NVE dynamics with good energy conservation, a GPU and CPU
> simulation started from the same starting conditions will eventually
> diverge because the system is chaotic and floating point round-off errors
> are enough to trigger this divergence.
>
>
>> Also i would like to know if i can compare values (like free energy) two
>> simulation ; one run on sander and other run on pmemd(cuda)?
>>
>
> Yes.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue Jul 15 2014 - 21:00:02 PDT
