On 7/22/13 1:20 AM, Kavyashree M wrote:
Dear users,
While running a ligand bound MD using AMber03 force field. I got the
following error
after ~ 4.9 ns
The initial cell size (1.247705) is smaller than the cell size limit
(1.586683), change options -dd, -rdd or -rcon, see the log file for details
Initially I ran using 64 nodes (till 3.3ns). later on I shifted the
trajectory to another
machine and ran using 8 cores. It ran fine till 4.926ns. Suddenly it
stopped with the above error.
Kindly provide some guidance.
You can't necessarily parallelize a system across any arbitrary number of cores.
The DD algorithm sets certain size limitations on the cells, which you are
violating during the simulation. A slight reduction in the number of cores
should solve the issue (though you can't restart from a checkpoint and may have
to start the run over).
For a more detailed explanation of the error message, check the archive - the
algorithm, the settings, and factors governing cell size have all been discussed
before in reference to the same error.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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