Can you tell us more about what you're simulating? Any nonstandard
parameters? For implicit solvent, which model and which radii set?
NaN is bad regardless of whether the simulation stops or not. When you say
sander. MPI and pmemd.MPI work, which code did not work? Was it on cpu or
gpu?
On Thu, Jun 20, 2019, 9:35 AM Paula Mihaljevic-Juric <
paula.mihaljevic-juric.polytechnique.edu> wrote:
> Hi!
>
> I am trying to run MD simulation in implicit solvent.
>
> I have tested the script on my desktop computer where for some results I
> would obtain NaN, but the simulations would not stop. Both sander.MPI and
> pmemd.MPI worked fine.
>
> However, when I am trying to use the same script on a supercomputer, the
> simulation crashes with the error NaN(s) found in the input coordinates
> while using pmemd.MPI. The simulation does not crash when using sander.MPI.
>
> What am I doing wrong? How can I fix this?
>
> Thanks
>
> Paula
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 20 2019 - 07:00:04 PDT
