ok sir.
I understand.
Thank you very much for your valuable suggestions.
thanking you
mary
On 7/16/14, Scott Le Grand <varelse2005.gmail.com> wrote:
> Just adding that each trajectory is just a single sample out of a huge
> posterior distribution given the input parameters and data as their prior.
>
> To get a better idea of the long-range behavior, you need to sample that
> distribution not just rely on a single data point...
>
>
>
>
> On Wed, Jul 16, 2014 at 10:03 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
>
>> Hi Mary,
>>
>> To offer a little extra info here. There is no 'problem' with the random
>> number stream being different, it just means that the random friction
>> forces applied by the Langevin thermostat will be slightly different, this
>> leads to a divergence in the trajectories - it will not however affect any
>> statistical results. If you want to observe the effect that differences in
>> the random number stream have on a trajectory then you can just run two
>> CPU simulations (with ig=-1) and compare those. You will see the magnitude
>> of the differences should be equivalent to what you see for the GPU run
>> compared with the CPU run.
>>
>> The take home message is that no single trajectory in its own right should
>> be considered to be definitive.
>>
>> All the best
>> Ross
>>
>>
>> On 7/15/14, 8:29 PM, "Mary Varughese" <maryvj1985.gmail.com> wrote:
>>
>> >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 Wed Jul 16 2014 - 22:00:02 PDT
