Ranjani Krishnan wrote:
Hi,
I have noticed that I cannot reproduce MD runs exactly -- running the
exact same .tpr file again gives different results. From previous posts,
I have seen some explanations for this. However, if I do AFM pulling
simulations, I am able to reproduce them exactly – running the same
simulation twice gives identical results.
Why is it possible to reproduce runs with AFM pulling, but not otherwise?
Because there's a source of randomness with your other ones that isn't
present for the AFM ones. Without knowing your compute configuration,
.mdp options and/or grompp command line, we're hard-pressed to say why.
Also, check out http://wiki.gromacs.org/index.php/Reproducibility
Mark
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