it could be changes to the box during equilibration, and a restart may work
as the message suggests.
or, it may be high energies are making the system large.
look at your mdout file and see if the energies are getting high.
On Thu, Dec 3, 2020 at 2:37 PM angad sharma <angadsharma54.gmail.com> wrote:
> I am running a simulation on dsDNA. It runs well till minimization and
> heating but as it starts for the equilibration process within a minute it
> stops by showing the following 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.
>
> For the above process the command was this:
> pmemd.cuda -O -i eq.in -o eq.out -p dna1.prmtop -c heat.rst -r eq.rst -x
> eq.mdcrd -inf eq.mdinfo
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Received on Thu Dec 03 2020 - 13:00:02 PST
