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
Received on Fri Jun 28 2002 - 02:17:20 PDT
