[AMBER] System blows up when simulating under npt

From: Amit Sharma (Asstt. Prof., MCARS) <"Amit>
Date: Tue, 24 Nov 2020 16:34:38 +0530


I trying to simulate protein having of FMN Cys adduct.

When running md using nvt and positional restraints of 0.5 kcal mol-1 A-2
on the protein, the system remains fine.

But as I switch to npt and remove all the restraints system blows up and
water molecules start flying away.

Error message is as follows:

"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."

Can anyone suggest how to deal with this?

Thank You,


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Received on Tue Nov 24 2020 - 03:30:02 PST
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