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 - 12:00:02 PST
