[gmx-users] node decomposition' problem
Justin A. Lemkul
jalemkul at vt.edu
Mon Jul 9 22:28:53 CEST 2012
On 7/9/12 4:25 PM, Justin A. Lemkul wrote:
> On 7/9/12 4:23 PM, Thales Kronenberger wrote:
>> I'm trying to run a kinase (what means that I had ATP - large charged
>> group) energy minimization and then MD.
>> But when I put my protein together with its ligands I gotcha the
>> follow error message:
>> "There is no domain decomposition for 6 nodes that is compatible with
>> the given box and a minimum cell size of 6.47943 nm
>> Change the number of nodes or mdrun option -rdd
>> Look in the log file for details on the domain decomposition"
>> I read about in gromacs forums and I can force the thing's running
>> with the option nt 1 (one node...).
>> My problem is that I still want to run in parallel. Is it still that
>> possible for my system or I'm doomed to the 1 core simulation
> The minimum charge group size depends on a whole host of factors:
*Edit* "minimum domain decomposition cell" - I don't know where "charge group"
> The large size you have obtained indicates there are likely problems with the
> .mdp file, topology, or both.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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