[gmx-users] segmetation fault and inconsistent shifts

[liu xin]

Hi David,

Thank you for your suggestion!

But I heard that there's some bugs to make hole with the later versions (is
it true?), so I choosed 3.1.4 to make hole.
I also installed 3.2.1, so I inserted the protein to the bilayer with a
hole, generated with 3.1.4. Then I  tried to minimize this system with 3.2.1,
I got the following error messages when I did mdrun:

Warning: 1-4 interaction between 41 and 51 at distance larger than 2 nm
These are ignored for the rest of the simulation
turn on -debug for more information
Fatal error: ci = -2147483648 should be in 0 .. 2365 [FILE nsgrid.c, LINE
218]

Could you tell me what to do with it?

Thanks in advance!

On 12/8/05, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> liu xin wrote:
> > Dear gmx-users;
> >
> > When I tried to minimize my lipid/protein system I got a "segmetation
> > fault" error message and the mdrun program stopped, then I  checked the
> > em.log file found there was a warning "There were 2 inconsistent shifts.
> > Check your topology". Did this warning cause the stop?.
> >
> > I searched this forum and did as told before: to add a line "pbc = xyz"
> > to my em.mdp, and export GMXFULLPBC = 1. But I still got this two
> > messages. I started the mdrun like $/home/xin/program/.../mdrun, and I
> > export like $export GMXFULLPBC, did I do it in a wrong way? My system is
> > SUSE 9.0, GMX 3.1.4, I am new to GMX and Linux, could anybody so kind
> > tell me how to over come this problem?
> please upgrade gromacs
> >
> > Thanks in advance!
> >
> > Liu Xin
> >
> >
> > ------------------------------------------------------------------------
> >
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>
> --
> 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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