On Mon, Apr 10, 2017, giulia palermo wrote:
>
> it's the first time I see something similar with AMBER. AFter a certain
> number of steps the energies are vertiginously going up
Do you have any non-standard residues or ligands in your simulation? What
you see can happen if a hydrogen atom (with zero LJ parameters) can come
close to a negatively charged atom nearby.
Of course, there are other things that could be happening as well. It
sometimes is worth trying to restart the run that failed with a smaller step
size. And, trying an experiment that turns of GaMD seems worth trying as
well.
....dac
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Received on Tue Apr 11 2017 - 05:30:03 PDT
