[gmx-users] Re: segmentation fault with grompp
Justin A. Lemkul
jalemkul at vt.edu
Mon Feb 8 23:04:28 CET 2010
Quoting Gard Nelson <gardnersnake23 at gmail.com>:
> Ok, here's what i've got:
> Gromacs version 4.0.5.
> Both platforms are Linux, icc 10, fftw 3
> compile option: ./configure --enable-mpi
The vast majority of Gromacs programs (read: anything not called "mdrun") are
not MPI-enabled. Users have reported weird activity when using, for instance,
mpicc to compile non-MPI code, although I don't know enough about that to
specifically say that's the problem. I would advise following the installation
instructions on the Gromacs site exactly, using MPI-enable compilers for mdrun
only, to see if that fixes your issue.
> thanks for your help!
> Gard Nelson wrote:
> > Hi all,
> > I'm trying to simulate a solvated membrane using Berger's lipids. When
> > I run grompp, i get the following error:
> > checking input for internal consistency...
> > processing topology...
> > Opening library file ...lipid.itp
> > Opening library file ...nb_lipid.itp
> > Opening library file ...bon_lipid.itp
> > Opening library file ...ff_dum.itp
> > Segmentation fault (core dumped)
> > I've tried this on two different machines with two different ff_dum.itp
> > files with the same results. Moreover, I've never touched the ff_dum.itp
> > file. I have modified the other forcefield files, both to include
> > Berger's lipids as well as other non-standard residues. It runs fine
> > with solvated proteins, but this is the first time I've run a system
> > with the membrane, so i'm guessing the error is coming from there. I've
> > looked through my files and cant find any errors. Does anyone have any
> > ideas of what might be causing this?
> Lots of things. But to get better help, you'll have to provide some more
> 1. Gromacs version
> 2. Platform
> 3. How Gromacs was compiled (commands, compilers used, etc)
> > Thanks
> > Gard Nelson
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul at vt.edu | (540) 231-9080
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