[gmx-users] Load imbalance and Y size error

nikhil damle pdnikhil at yahoo.co.in
Thu Oct 8 08:14:27 CEST 2009

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 ?


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