AMBER Archive (2002)

Subject: EWALD BOMB (The system has extended beyond ...)

From: Michael Jakusch (michael.jakusch_at_pharma.anbi.ethz.ch)
Date: Fri Jun 28 2002 - 04:17:20 CDT


Dear AMBER users,

I'm trying to run some very crude MD simulations on a nonperiodic
system with water cap using AMBER 7. I observe sander frequently dying
with a message like this:

 Frac coord min, max: -0.00035776025 0.822900712
 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

Unfortunately, restarting _doesn't_ help - I get the same error even
earlier (e.g after 640 steps instead of 1320 in the previous run).

My input files look like this:

-> &cntrl
-> imin=0,
-> ntx=5
-> nstlim=100000, dt=.002
-> ntpr=10,ntwe=10,ntwx=100
-> ntc=2,ntf=2
-> ntb=0, cut=12
-> ntt=1, tautp=.2
-> ibelly=1, ntr=1
-> &end
-> &ewald
-> eedmeth=5
-> &end
-> restrained
-> 25.0
-> RES ... ...
-> RES ... ...
-> END
-> END
-> belly
-> RES ... ...
-> RES ... ...
-> END
-> END

Can anybody advise me how to circumvent this problem?

Kind regards

     Michael

-- 
Dr. Michael Jakusch

ETH - Swiss Federal Institute of Technology Department of Applied Biosciences Winterthurerstrasse 190 CH-8057 Zürich Switzerland Phone: +41.1.635 60 71 Fax: +41.1.635 68 84 email: michael.jakusch_at_pharma.anbi.ethz.ch