[gmx-developers] MPI crash with ghost molecules

Jason de Joannis jdejoan at emory.edu
Thu Nov 2 18:27:45 CET 2006

I start with a 128 DPPC bilayer. I also have 128 D8PC which I turn off 
at the beginning of the simulation. When I say 'turn off' I mean that 
the atom types are set to 13 (same as HW) and the charges are zeroed. 
Therefore these molecules will only experience their own intramolecular 
forces and will not exert any influence on the system. They are 
probably absent from the neighbor lists too right?

Now. During the simulation (in between move_x and ns) I pick a DPPC 
molecule and turn it off while turning on a corresponding D8PC 
molecule. The D8PC coordinates and velocities are mapped onto those of 
the outgoing DPPC.

This is successful in single-thread runs but fails in MPI np=2 mode. 
For example after such a conversion on step 50, the LINCS constraints 

Any thoughts?

\ Jason de Joannis  \
\ Emory University  \
  \ jdejoan at emory.edu \
   \ 404-402-1332      \

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