[gmx-users] re:Membrane Peptide+ DPPC+ Water simulation

David van der Spoel spoel at xray.bmc.uu.se
Mon Aug 23 15:06:31 CEST 2004

On Mon, 2004-08-23 at 14:31, pandey at bioinfo.ernet.in wrote:
> Hi Group,
> Thanks to John Shims, I have been able to run grompp command with modified
> ffgmxnb.itp and ffgmxbon.itp
> But, as usual I am again getting error while grompp in shuffle mode, it is
> get terminated with "segmentation fault"
> I am running with following commands:
> ------------------------------------------------------
> grompp -np  8 -shuffle -sort -f em.mdp -c cla_b4ion.gro -p cla_1.top -o
> b4em.tpr;
> mdrun_mpi -np 8 -shuffle -sort  -s b4em.tpr -c minimized_cla.gro -o
> minimized_cla.trr -e
> ------------------------------------------------------------
Which gromacs version?

Try to start without shuffle and sort. For production sort is not
proactical anyway (because there is no way to unsort).
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://xray.bmc.uu.se/~spoel

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