[gmx-users] Option -shuffle, -sort, -np missing in grompp in version 4.0?

David van der Spoel spoel at xray.bmc.uu.se
Sat Oct 11 17:06:16 CEST 2008

Martin Höfling wrote:
> Am Samstag, 11. Oktober 2008 schrieb Lee Soin:
>> The command grompp used to have options -shuffle, -sort and -np, but it
>> seems that they appear no more with version 4.0?
> These options were used for particle decomposition in the tpr file. Gromacs 4 
> default method is domain decomposition, but as far as I remember, PD is still  
> optional. The options can be set during run-time so that a tpr input file 
> itself is independent of the parallel setup during runtime (the output may 
> depend upon the runtime environement). Thus you should find all options in 
> mdrun. The -np switch isn't required anymore (for mpi).
> Please correct me if I'm wrong...

These options have been removed indeed. Domain decomposition is much 
more efficient than particle decomposition. Therefore PD is useful only 
in special cases.

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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