[gmx-users] Error mesage

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 21 17:03:38 CEST 2011

Tanos Franca wrote:
> Dear gmx users,
> Does someone know how to deal with the error mesage bellow ?

The DD geometry depends upon the configuration of the system, constraints 
applied, cutoffs, and any other special restraints (like distance restraints) 
that may be present.  The error message suggests that you decrease the number of 
DD cells, which I would suggest you try.  This makes each DD cell larger and 
thus capable of handling longer interactions.  There are minimum size limits 
defined in the log file; if the system changes much then these can become invalid.


> With my best regards,
> Tanos C. C. Franca.
> Program mdrun, VERSION 4.5.4
> Source code file: domdec_con.c, line: 693
> Fatal error:
> DD cell 2 1 0 could only obtain 273 of the 275 atoms that are connected 
> via constraints from the neighboring cells. This probably means your 
> constraint lengths are too long compared to the domain decomposition 
> cell size. Decrease the number of domain decomposition grid cells or 
> lincs-order.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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