Re: [AMBER] gpu and cpu runs

From: Jason Swails <>
Date: Tue, 15 Jul 2014 19:08:14 -0700

On Tue, Jul 15, 2014 at 6:57 PM, Mary Varughese <>

> sir,
> above mentioned topic link:
> 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)?



Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 15 2014 - 19:30:02 PDT
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