nikhil damle wrote:
Hi all
I am trying to simulate a system of 3168 atoms in vacuum in PBC
box (-d=0.9 nm). Since there are no solvent molecules, i am unable to
neutralise the system using addition of ions (Hence system has +3
charge). As soon as i start the MD run after putting the whole system in
box, there is imbalanced force of 80% due to which right in the
beginning, dynamic load balancing is turned on. But even after this,
there is ~22% loss of performance and after certain steps MD crashes
saying :-
"Fatal error: The Y-size of the box (4.618413) times the triclinic skew
factor (0.866051) is smaller than the number of DD cells (2) times the
smallest allowed cell size(2.000000)"
Can anyone explain the origin of this error and how to deal with it ?
Try running with one processor to see if it's your system or the domain
decomposition algorithm that is the problem. DD doesn't necessarily cope
well with highly heterogeneous distributions of particles.
Mark
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