However, if this happened after running equilibrium MD, I'd be inclined to
think that the [ reason ] is a concern: something about your pulling setup
has thrown a wrench in the system and it has now blown up.
On Mon, Aug 27, 2018 at 1:49 PM David Cerutti <dscerutti.gmail.com> wrote:
> 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 - 11:00:02 PDT
