Dear all The last days I switched from Gromacs 3.3.3 to Gromacs 4.5.3, but I experience some difficulties when running in parallel.
Initially, my simulation box has dimensions : * 3.30507 2.67145 41.15800* and it consists of 25 polymers chains with 50 beads/chain When I run NVT using 8 or 16 cores, everything is working fine, but when I compress it to dimensions: *3.30507 2.67145 10.64441* and try again to run NVT in 8 cores, I have the following error message: *There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 2.5 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings* As I saw this is well known error, but I can't understand how to fix it :-) >From what I understood, this is happening because* I use constrains in all the bonds of my system* In my .log file I see the following: *Initializing Domain Decomposition on 8 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Minimum cell size due to bonded interactions: 0.000 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 2.000 nm Estimated maximum distance required for P-LINCS: 2.000 nm This distance will limit the DD cell size, you can override this with -rcon Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 8 cells with a minimum initial size of 2.500 nm The maximum allowed number of cells is: X 1 Y 1 Z 4* , but I can't understand how to use -rcon or -dds in order to fix my problem Any suggestions? Thanks in advance Chrysostomos
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