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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 15 2014 - 19:30:02 PDT
