[gmx-users] shuffling around

Christian Kandt kandt at bph.ruhr-uni-bochum.de
Tue Apr 2 12:10:35 CEST 2002

Hi there!

I just did an parallel MD-run with the shuffle option activated. The
increase in speed is notable and quite pleasing.

To my surprise that run finished with all my system components being
completely resorted. I used to have three blocks of data: protein, lipid
and water. But now I ended up with six: Monomer1, some water, some
lipid, monomer 2, some water, some lipid.... etc.  All residue numbers
have been reassigned, wich is quite annoying for analysis.

Is all this due to the activated shuffle option? How can I undo these
shuffling effects to get back my old sorting order and residue

Thanks in advance,

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