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

[pandey at bioinfo.ernet.in]

Hi,
I am using Gromacs-3.1.4, mpi version. In past i have been able to run
production run with same command with sort and shuffle. It has been
successful while peptide+water. But, when i try with peptide+water+DPPC
system, its giving error.

Thanks and Regards
Om Prakash
Bioinformatics Center
University of Pune
Pune
India

> 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.
> ________________________________________________________________________
> 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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