AMBER Archive (2000)

Subject: Re: [pavan@bnpi.com: 'Coordinate resetting in amber6']

From: Michael Crowley (crowley_at_scripps.edu)
Date: Wed May 17 2000 - 18:08:26 CDT

It is possible that it is due to the cell dimensions not being
specified in the correct way after the minimization.
The coordinate output from a minimization does not
have the cell information in it, that info is
normally after the velocities and the minimization
output does not have velocities in it.

This error message occurs when the array sizes for
the ewald grid are exceeded, sometimes because of
an expanding system. However, these dimensions
are determined at the start from the initial cell
sizes, wherever gibbs or sander can get them. If
the array dimensions for the wrong sized box, then
you get the error.

I am not familiar with gibbs pme, but in sander
the solution would be along these lines.
The best bet is to look at the end of the
restart file from the simulation before the
minimization and use that cell information

  .
  .
  .
   1.4804489 1.0506761 0.0278816 0.2718482 -0.1646505 -0.4032318
   0.5833464 -0.6189719 0.1136061 0.5446580 -0.7859168 -0.2447396
  -0.0527578 -0.1019692 0.2010712 -0.1265974 0.2800501 0.5986397
  -0.9036080 -0.8382727 -0.5021025
  19.7550000 19.7550000 19.7550000 90.0000000 90.0000000 90.0000000

in the ewald info at the end opf the PIN file:

  .
  .
  .
  almda = 1, almdel = 0.05, isldyn = -3, idifrg = 1,
  nstmeq = 500, nstmul = 500,

 &end
19.755 19.755 19.755 90.0 90.0 90.0
20 20 20 4 1 0
0.00001

I hope that helps.
Mike