[gmx-users] shuffle and sort???

Arvid Soederhaell arvid at fmp-berlin.de
Tue Sep 23 11:58:01 CEST 2003

Dear all 

I have just encountered a problem with the -shuffle and -sort  flags for
grompp for MPI runs. I started my simulation on a single node, and then I
went over to run in paralell (2 nodes). I have just realized that the
molecules appear in a new order in the output .gro file (from the
paralell run) than in the output from the single node run. This cause a
big problem in reading and processing the trajectory, and also restarting
the simulation, since the topolog doesn't match the gro-file any more. 

I guess this has to do with -shuffle and -sort but I don't know... 

What has happened is that before the paralell run I have first 64 DPPC
molecules and then the water listed in the gro file (and in the top file).
After the paralell run I have 32 DPPC molecules, then half of the water,
and then another 32 DPPC molecules followed by the remaining water. 

For this system I cannot calculate the membrane order parameters, for
example, because the atoms have different numbers in the single-node and
multiple-node output...
How to get this right again????


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