Hi Roma,
did you run a minimizartion before the MD? Try minimizing with pmemd instead of pmemd.cuda. Please share your output file.
Best,
Andy
> Am 17.02.2018 um 05:07 schrieb Roma Mukhopadhyay <roma1988.nmsu.edu>:
>
> Dear all,
>
>
> I have been trying to simulate my molecule of interest using barostat=1, which uses Monte Carlo Barostat algorithm in pmemd cuda, but the simulation keeps on crashing within 0.5 ns giving NaN values for energy. However when I run the same simulation in pmemd platform it works fine. Has anyone faced the same issue?
>
>
> Is their any specific way to overcome this issue in pmemd cuda platform? I have seen if I use Berendsen algorithm this problem does not arise at all.
>
>
> Any and all help is highly appreciated.
>
>
> Thanks
>
> Roma
> _______________________________________________
> 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 Sat Feb 17 2018 - 00:30:02 PST
