On Wed, Feb 11, 2015 at 7:09 AM, Kshatresh Dutta Dubey <kshatresh.gmail.com>
wrote:
> Hi Jason,
>
> Thanks for your reply. The error is :
>
> ERROR: Calculation halted. Periodic box dimensions have changed too much
> from their initial values.
> 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.
>
This tells you what to do, and gives you 2 options. I suggest following
its advice.
You should also plot the density (you can use mdout_analyzer.py for this)
and make sure that it is steadily increasing during the simulation before
the simulation terminated. This tells you that the system hasn't "blown
up", but is rather contracting too much for the cell decomposition to
accommodate.
Note you may have to do this several times before the density stabilizes
and the system size stops shrinking.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Feb 11 2015 - 05:00:02 PST
