[AMBER] Error in themodynamic integration with PMEMD.CUDA

From: HOCHEOL LIM <ihcdatabank.gmail.com>
Date: Fri, 22 Nov 2019 00:06:28 +0900

Dear All,


I would like to simulate tri-peptide with GPU-TI (PMEMD.CUDA).

However, I got error message when I used pmemd.cuda.
When I changed pmemd.cuda (gpu) to pmemd (cpu), it worked.

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
  is a long way from an equilibrated density.

  Alternatively you can run with the CPU code until the density has
  and then switch back to the GPU code.

I attached 'in' and 'out' files in 0.0 steps in TI simulation.

What should I do for simulating the system with pmemd.cuda ?

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Received on Thu Nov 21 2019 - 07:30:02 PST
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