[gmx-users] shuffle option

[David van der Spoel]

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 
decomposition.

-- 
David.
________________________________________________________________________
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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