[gmx-users] Ewald summation: segmentation fault!

David spoel at xray.bmc.uu.se
Wed Apr 30 19:13:01 CEST 2003

On Wed, 2003-04-30 at 18:21, Vincent Ballenegger wrote:
> Bert de Groot wrote:
> >I'd be surprised if your system would run. You have opposite charges
> >and no vdw parameters, ie the particles can approach each other to
> >zero distance very rapidly, causing the electrostatic energy (and forces)
> >to explode. Strange that you don't run into this problem with PME or PPPM
> >though...
> >
> Sorry, I forgot to say that I keep the 2 ions fixed in space by setting
> their velocity to zero at every time step. The same problem of segmentation
> fault occurs in the original version of gromacs, in which case I use the
> freeze option:
> freezegrps               = Na+ Cl-
> freezedim                = Y Y Y Y Y Y
> Vincent
It's weird anyway. We appreciate people doing this kind of tests, since
we can't do everything...

The fact that your md.log file ends in the middle of printing is not
indicative of anything (check the filesize, it is probably a multiple of
4096, i.e. file buffering in action).

You may want to rerun in the following way:
setenv LOG_BUFS 0
mdrun -debug

Please report back what happens.

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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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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