[gmx-users] Segfault on energy minimization
mark.j.abraham at gmail.com
Fri Dec 12 20:30:37 CET 2014
The "Fmax= 2.35818e+10, atom= 214" in the output says you are
http://www.gromacs.org/Documentation/Terminology/Blowing_Up, likely because
you've constructed initial conditions that don't make sense, leading to
forces many orders of magnitude higher than you probably intend. Start with
the simplest system you can think of, to debug your topology, force field
and initial coordinates.
On Fri, Dec 12, 2014 at 8:05 PM, Diego Muñoz G. <diego.munoz.g at ug.uchile.cl>
> Dear Gromacs users,
> I'm trying to launch a MD calculation involving silver atoms, but when I
> run the
> energy minimization gromacs crashes into a Segmentation Fault. This is:
> when I type:
> mpirun -H nodo1 -np 8 gmx_mpi mdrun -deffnm solvent_test
> y get this output: http://pastebin.com/JeNqVFgc
> I've tried rebuilding the topology file, reinstalling gromacs, and testing
> the same run on
> another computer obtaining the same result.
> Does anyone knows what could I have done wrong?
> Im using Gromacs 5.0.2 with MPI support on Archlinux.
> Diego Muñoz G
> Departmento de Química
> Laboratorio Fisicoquímica Molecular
> Facultad de Ciencias
> Universidad de Chile
> Fax: 562-22713888
> Tel: 562-29787342
>  http://pastebin.com/JeNqVFgc
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