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
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Received on Wed May 22 2024 - 05:00:02 PDT
