AMBER Archive (2007)

Subject: Re: AMBER: Sander Error

From: Phineus Markwick (phineus_at_pasteur.fr)
Date: Fri Jun 29 2007 - 10:45:18 CDT

Hi,

I think you've probably made the direct space sum cut-off (CUT) for the
Particle Mesh Ewald routine
larger that 1/2 of the size of the unit cell. The necessity for periodic
boundary conditions in PME arises
from the fact that the long range sum is calculated in Fourier space.
However, the direct space sum should only
be performed over atoms in the central unit cell and not include
interactions between atoms in the central unit cell and periodic
"images" of these atoms.Therefore, sander is telling you that you have
to increase the size of your solvated box by 60 angstroms for the cutoff
value that you have chosen.

phin.

 
Colby C schrieb:
> Frac coord min, max: -2.0586063485058166E+7 2.058606450492667E+7
> 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
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