[gmx-users] shuffle option

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 19 15:33:51 CET 2006

Lubos Vrbka wrote:
> hi guys,
> it is written in the manual that using -shuffle is beneficiary for 
> multiprocessor runs. there is however also written that
> "the output trajectories will be also shuffled. grompp writes an index 
> file which can be used to deshuffle the trajectories"
> what exactly does this mean? when i view the trajectory from such a run 
> it looks ok...
> is it so that number of atoms differ between shuffled and unshuffled 
> trajectory?
> thanks for clarification. regards,
just the order of the molecules is mixed up. as long as you stick with 
this ordering it is fine. but if you want to go from e.g. 12 to 6 
processors you may need to reshuffle.

anyway, shuffle can be undone but not sort.

in gromacs 4.0 these options will disappear and we'll have domain 

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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