Thank you very much
There are no non-standard residues in the simulation.
I'll try these strategies as well.
Giulia
2017-04-11 5:12 GMT-07:00 David Case <david.case.rutgers.edu>:
> 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 - 15:00:04 PDT
