AMBER Archive (2005)

Subject: AMBER: "The system has extended beyond" error

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Mar 29 2005 - 16:28:35 CST


Dear All,

I am trying to run a simulation for an ethane molecule in gas phase.
I created this ethane molecule in xleap, and it is for ethane ->
methane perturbation. The input file I have is as follows:

--------------
200 ps simulation with lambda = 1
 &cntrl
  imin=0,
  ntx=1,irest=0,
  ntpr=250,ntwr=1000,ntwx=250,
  ntc=1,ntf=1,ntb=0,cut=10,
  igb=0,
  ntr=0,
  nstlim=200000,dt=0.001,nscm=1000,nrespa=1,
  ntt=3,gamma_ln=1,tempi=300,temp0=300,ig=233,
  ntp=0,taup=1,pres0=1,
  icfe=1,clambda=1,klambda=6
 /
--------------------
Before running this job, I minimised this structure. In any case, when the
above job is run, I am getting an error at 152.750 ps. Here is the error:

--------------------
 NSTEP = 152750 TIME(PS) = 152.750 TEMP(K) = 316.18 PRESS =
0.0
 Etot = 10.3009 EKtot = 5.6547 EPtot =
4.6462
 BOND = 3.4010 ANGLE = 1.1054 DIHED =
0.1398
 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
0.0000
 EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------

 Frac coord min, max: -4.942607998894864E-004 0.500000000000000
 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
------------------------------------

As far as I understand, the above error is saying that the molecule is out
of the virtual box sander has created. Does that mean that it is not
important? I dont use any boundary. This is just for testing on something.
I will appreciate if someone can give me more info about this error.

Best,

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -                              -
  - University of Rochester      -                              -
  - Hutchison Hall, # B10        -                              -
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) -
  - http://www.pas.rochester.edu/~yildirim/                     -
  ---------------------------------------------------------------

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