On Sat, Feb 17, 2018, Roma Mukhopadhyay wrote:
>
> Attached are the two production run files with exact same input but the
> energy values are different, and this difference is based on the random
> seed number, which I still don't understand why should influence my
> energy (I am using ntt=1). If I use the same ig number I get the exact
> same value, but still the system crashes with NaN.
> > 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?
One guess is that you are hitting an error in pmemd.cuda with small box sizes:
Box X = 27.978 Box Y = 27.978 Box Z = 27.978
Alpha = 109.471 Beta = 109.471 Gamma = 109.471
Could you post the prmtop and starting coordinates? I think Dave Cerutti
(cc-ed here) knows what may be going on. Even if (or especially if) my guess
is wrong, it would be very helpful to be able to reproduce the problem.
[If I am correct, the barostat use may be exposing the problem, but not really
causing it.]
...thx....dac
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Received on Sun Feb 18 2018 - 17:30:02 PST
