[AMBER] Calculation halted on pmemd.cuda

From: 库米尔 <418025.mail.dhu.edu.cn>
Date: Sat, 27 Mar 2021 08:10:06 +0800 (GMT+08:00)

Dear Amber community,

My simulation frequently halts on cuda with the following error message after I have done series of minimization and equilibration of system:
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.

And with little experience I have got with my system, whenever I encounter such errors I have to go back to the packing stage to increase the number of molecules/atoms in the box( undesirable) or use slow sanders to overcome such a challenge which admittedly is very unsustainable for the kind of system am dealing with. In fact it is causing me a lot of headache and discomfort. Is there better way to fix this challenge once and for all?

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Received on Fri Mar 26 2021 - 17:30:02 PDT
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