[gmx-users] shuffle/sort problem

David van der Spoel spoel at xray.bmc.uu.se
Mon May 27 10:03:40 CEST 2002

On Mon, 27 May 2002, Lynne E. Bilston wrote:

>I'm simulating a largish system using the mpi version of Gromacs, on RH7.2 
>linux dual athlon machines. My system runs just fine if I run it over 
>multiple cpus, without the shuffle and sort options, with no error 
>messages, albeit more slowly. The results look sensible. But when I use the 
>shuffle/sort options, I get 1-4 interaction messages at the start of the 
>simulation, and nan energies. This happens with the exact same input 
>options and co
Sounds like you are missing shuffled and unshuffled coordinates. Once you
have done a run with shuffling, the coordinates stay shuffled. This is a
known defeciency. That means you can not combine your confout.gro from a
shuffled run with your original topology. grompp will give you error
messages about mismatch between names in topology and coordinate file.
You can use the deshuf.ndx file to de-shuffle the order in your
gro/trr/xtc files. This problem will be fixed in a forthcoming version of

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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