[gmx-users] Segfault on energy minimization

[Diego Muñoz G.]

I caught the problem, i had my silver atoms too tight inside the box causing 
them to collide in the boundaries. Many thanks Sr. Abraham.

On Friday 12 December 2014 20:30:29 Mark Abraham wrote:
> Hi,
> 
> 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.
> 
> Mark
> 
> On Fri, Dec 12, 2014 at 8:05 PM, Diego Muñoz G. <diego.munoz.g at ug.uchile.cl>
> wrote:
> > 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[1]
> > 
> > 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
> > 
> > --------
> > [1] http://pastebin.com/JeNqVFgc
> > --
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-- 
Diego Muñoz G
Departmento de Química
Laboratorio Fisicoquímica Molecular
Facultad de Ciencias
Universidad de Chile
Fax: 562-22713888
Tel: 562-29787342