[AMBER] Calculation halted while running simulation

From: angad sharma <angadsharma54.gmail.com>
Date: Fri, 4 Dec 2020 01:06:21 +0530

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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 03 2020 - 12:00:02 PST
Custom Search