Hi all, I'm trying to run a parallel Job for a system of dummy atoms that arranged as 2 surface (each is 6X6 atom surface- with bonds that i defined between them) the system is solvated in a box of dimensions 4.5nm X 6.5nm X 4.5nm with salt, minimized and equlibrated fine.
however, when trying to execute parallel Job i get the following domain decomposition error: *------------------------------------------------------- Program mdrun, VERSION 4.0.7 Source code file: domdec.c, line: 5888* *Fatal error: There is no domain decomposition for 2 nodes that is compatible with the given box and a minimum cell size of 3.37646 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition -------------------------------------------------------* ** ** i read the relevant paragraphs on the manual regarding domain decomposition , but remained confused. my question is How do you think i should solve it, and what are the thumb rules for the use of the -rdd and -dds flags? (i think that i did not quit understood from the manual how are the 2 flags relate to the parameters of my system) Thanks, Amir
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