It's detailed because I was involved :-)
On Mon, Aug 27, 2018 at 8:09 AM David A Case <david.case.rutgers.edu> wrote:
> On Mon, Aug 27, 2018, M RCC wrote:
>
> > Why am getting the following error, while running the pulling step in
> > umbrella sampling?
> >
> > Your system density has likely changed by a large amount, probably from
> > starting the simulation from a structure a long way from equilibrium.
> >
> > [Although this error can also occur if the simulation has blown up for
> > some reason]
> >
> > The GPU code does not automatically reorganize grid cells and thus you
> > will need to restart the calculation from the previous restart file.
> > This will generate new grid cells and allow the calculation to
> continue.
> > It may be necessary to repeat this restarting multiple times if your
> > system is a long way from an equilibrated density.
> >
> > Alternatively you can run with the CPU code until the density has
> > converged and then switch back to the GPU code.
>
> Wow: by Amber standards, this is an incredibly detailed explanation.
> What part of it don't you understand? Since people on the list know
> nothing about your system, we can't provide an explanation for *why* you
> density has changed by a lot. Do you think you system is
> well-equilibrated?
>
> Anyway, there are at least two suggested workarounds above: restart the
> calculation with the GPU, or use the CPU version to get to a converged
> density. Visualizing your system is also always a good thing to do when
> things go wrong.
>
> ...good luck....dac
>
>
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Received on Mon Aug 27 2018 - 11:00:01 PDT
