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 - 05:30:03 PDT
