Re: [AMBER] simulation energies are exploding

From: David Case <david.case.rutgers.edu>
Date: Tue, 11 Apr 2017 08:12:59 -0400

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
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