[AMBER] Incomplete trajectory due to calculation halted error

From: Razil Tahir <raziltahir.hotmail.com>
Date: Tue, 8 Jun 2021 19:07:35 +0000

Dear all,
I have run a production simulation in several steps of 100ps each which the output of the 100ps step will be used in the subsequent steps.
I found out that there are several steps that got this 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.”

 However, the output from these unfinished steps is used as the input for the subsequent steps.

My question is why the subsequent steps continue and the outputs from unfinished steps can be used as the input file for the next step even though it is incomplete?

Best Regards,

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Received on Tue Jun 08 2021 - 12:30:02 PDT
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