There are many possible causes and it's hard to say without knowing more. I
suggest checking the energies at the beginning of the restart - are these
reasonable? If there are not any printed, try reducing ntpr until you get
energies. if you still can't fix it, then share the output file so we can
see your setup.
On Wed, May 22, 2024 at 7:31 AM Priyasha Majee via AMBER <amber.ambermd.org>
wrote:
>
>
> Hello All,
>
> I am trying to do a simulation of a protein-DNA complex. I did 200ns
> production successfully. Now I want to extend the production to 500ns
> using the rst7 file I got in the 200ns production run but it's throwing
> an unlikely error.
>
> 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.
>
> I am not sure why this is happening midway through the simulation. Can
> someone help me with this?
>
> Thanks in advance
>
> Regards,
>
> Priyasha
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 22 2024 - 07:00:02 PDT
