AMBER Archive (2003)

Subject: problem about virtual box?

From: Youyi Peng (pengyo_at_UMDNJ.EDU)
Date: Thu May 01 2003 - 10:49:00 CDT

Dear AMBER fans:
  Last week I posted my problem about "the system has extended beyond
the extent of the virtual box" and I got some helpful answers.
Then I read the archive and found several similar posts to my problems.
It looks two ways to solve the problem: one to check
the trajectory and understand why it is changes so quickly, the other to
modify "extraboxdim" in nonper.h file. I visualized the MD trajectory in
moil-view and found the system shift a lot. My protein is a several
transmembrane-helix protein. I did in vacuo MD on the protein-ligand
complex. The last frame (at 236 ps) looks perpenticular to the first one
(viewed in moil-view). But if I superimpose two conformations in
InsightII, they look ok and the ligand still is in the binding pocket.
It looks to me the whole complex in vacuo moves fast during MD
simulation but the conformation of the complex doesn't change too much.
Doesn't anybody has the similar experience? what should I do next? Maybe
I need to modify the nonper.h file? By the way, which directory is
nonper.h in? Any suggestion is more than welcome.
  The following are the error message for the output file and my input
file for the MD simulation. I restarted the simulation and tried on both
SGI and linux machines, but the problem still exists. The only
difference is the job stopped at different time.
  Thanks a lot.
Error message:
Frac coord min, max: -2.1534132742728489E-06 0.7410054892789126
 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.
 EWALD BOMB in subroutine Routine: map_coords (ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error

 Input MD file:
dynamics w/o belly on protein, 9.0 cut, without constraints
 &cntrl
  nmropt = 0,
  ntx = 5, irest = 1, ntrx = 1, ntxo = 1,
  ntpr = 1000, ntwx = 1000, ntwv = 0, ntwe = 0,

  ntf = 1, ntb = 0,
  cut = 9.0, nsnb = 10, dielc=4.0

  ibelly = 0, ntr = 0,

  imin = 0,
  nstlim = 500000,
  nscm = 0,
  dt = 0.001,

  temp0 = 300.0, tempi = 300.0,
  heat = 0.0,
  ntt = 1,
  tautp = 2.0,
  vlimit = 20.0,
  ntc = 1, tol = 0.00001,
 &end

 &ewald
   eedmeth=5,
 &end