AMBER: sander bomb

From: janavi raghavan <>
Date: Tue, 3 Apr 2007 15:28:39 +0100 (BST)

In my md run i am getting a sander bomb.the error is as follows:
  Local SIZE OF NONBOND LIST = 1446256
   Frac coord min, max: 0.510295224658475 1.00159624388865
   The system has extended beyond
       the extent of the virtual box.
   Restarting sander will recalculate
      a new virtual box with 30 Angstroms
      extra on each side, if there is a
      restart file for this configuration.
   SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
   Atom out of bounds. If a restart has been written,
   restarting should resolve the error.
  in one of the previous explanations about the sander bomb (dated:5/12/2005)
  it was a periodic boundry system.i am using non-periodic boundary condition with 2 shells of water with the outer shell being constrained by a large harmonic potential.i am using nscm= 5000 ..........
  could you please tell me the reason for this ocurrence and also how i could rectify it.
  thanking you in advance:

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Received on Wed Apr 04 2007 - 06:07:44 PDT
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