Hi,
this is probably caused by some other problem in your system. Even in a
vacuum simulation Amber assumes an implicit (generously sized) box around
your system. This rarely has an effect, except when your system changes
its shape tremendously, that is if it
a) explodes due to bad contacts
or
b) has a very weird potential energy shape that causes huge conformational
changes in your minimization.
Visualize your system and check what the structure looks like before the
crash. If you are really sure that it behaves ok, restart your simulation
from the last restrt file, Amber will make a new virtual box based on the
new starting structure. Beware: In 99% of cases, this error means
something else is wrong and needs to be fixed first, which could be many
things, depending on your system.
As a side note: 100000 cycles of minimization in conj grad or steepest
descent mode will not really accomplish anything after cycle 1000 or so.
What is the purpose of your minimization to set the parameters like this?
Thomas
>> I am minimizing a sytem in vacuum with maxcyc=100000 and
>> ncyc=50000....the minimization does not complete in maxcyc...so I
>> tried to minimize the system again with the same input restarting from
>> the coordinates of the previous minimization. But, I get the following
>> error and the program exits:
>>
>> .... RESTARTED DUE TO LINMIN FAILURE ...
>> Frac coord min, max: -9.867200925854984E-002 0.889932643669276
>> 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
>>
>>
>> Whats the cause of the problem?
>
>
> -- Atom out of bounds, I would guess.
>
> It is you to know better how it happened with your particular system.
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Mon Jul 16 2012 - 09:30:03 PDT
