[gmx-users] Re: segmentation fault with grompp

[Gard Nelson]

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

thanks for your help!
Gard


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
information:

1. Gromacs version
2. Platform
3. How Gromacs was compiled (commands, compilers used, etc)

-Justin

> Thanks
> Gard Nelson
>
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