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

[David van der Spoel]

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