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.
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)?
thanking you
mary varughese
On Tue, Jul 15, 2014 at 9:13 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Tue, Jul 15, 2014 at 12:23 AM, Mary Varughese <maryvj1985.gmail.com>
> wrote:
>
> > Sir,
> >
> > This is a previos mail,
> >
> > Topic: different RMSF between CPU and GPU (Ross Walker)
> >
> > 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 am getting the same issue (15ns) runs are quite different. i thought
> > its due to ig=-1.
> > i have used ntt=3;
> >
> > So am i doing anything wrong.
> >
> > could do suggest any other option.
> >
>
> I think I recall the email you're talking about, but I certainly don't
> remember the minute details (specifically how different the RMSF was
> between the CPU and GPU). These kinds of references to past emails are of
> limited use when you don't provide a link to the archived copy.
>
> 2 comments:
>
> 1. It sounds like you're simply repeating this question, as though you
> don't trust the answer from that post. If you have evidence to suggest why
> the explanation in that email is not correct, give it and formulate a more
> complete question.
>
> 2. 15 ns is a very short simulation, and it's highly unlikely that any
> measurable properties have converged for any except the smallest of
> systems. You have no reason to expect that unconverged simulations will
> resemble each other.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue Jul 15 2014 - 19:00:02 PDT
