[gmx-users] segmentation fault on trjconv with deshuf

[Lynne E. Bilston]

>
>
>Hmm... Segfault are always really bad, but I just don't have time to debug 
>it right now.
>
>What I usually do when I run in parallel is to create a topology where the 
>molecules section at the end is the same order as the shuffled system, e.g.
>
>
>DPPC    10
>SOL       230
>DPPC     10
>SOL        230
>
>etc...
>
>This way you can use this topology instead and never care about undoing 
>the shuffling. If you don't remember the molecule distribution you can 
>just rerun grompp
>with the shuffle option and look at the way it distributes molecules over 
>CPUs.

Thanks. That will work in the interim. BTW, the segfault seems to be 
possibly related to the pdb output format. If I write out as trr, it's OK.

Cheers,

Lynne

>Cheers,
>
>Erik
>
>

________________________________________________________________________________
Lynne E. Bilston, PhD
Senior Scientist, Prince of Wales Medical Research Institute, and
Conjoint Associate Professor, Faculty of Medicine, University of New South 
Wales
Barker St, Randwick, NSW 2031 Australia
Tel: +61-2-9382-7924	Fax: +61-2-9382-2643
________________________________________________________________________________