Thanks.
It's interesting how such small differences can compound to totally
different conformations within a few ps (the energies are close though,
which one would expect at equilibration).
M
On Fri, Mar 22, 2019 at 4:29 PM Benson Muite
wrote:
> Hi,
>
> Yes, finite precision and order of compu
Hi,
Yes, finite precision and order of computations may not be respected by
the compiler. In most cases, they should be close, however much
analytical work remains in this area. A relevant paper (though there
are many others) is:
Collange, Defour, Grailaat and Iakymchuk
Numerical Reproduci
Hi Mark,
Thanks so much -- good to know that it's basically equivalent to different
starting velocities and I should expect them to be different.
I found this page that sort of explains it:
http://www.gromacs.org/Documentation/Terminology/Reproducibility
Out of curiosity, I was wondering if some
Hi,
The dynamic load balancing on by default for domain decomposition means
divergence happens by default. After a few ps it's logically equivalent to
starting from different velocities. See the GROMACS user guide for more
details on reproducibility questions!
Mark
On Fri., 22 Mar. 2019, 18:15 M
Hi all,
We set up replicate simulations (same starting mdp files and structures)
that ran across GPUs WITHOUT using the -reprod flag, but we set gen-vel to
no and used the same ld-seed value for both with the v-rescale thermostat.
They also ran on the same machine -- so from a deterministic point
