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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> >>
> >
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Received on Wed Jul 16 2014 - 10:30:02 PDT
