[gmx-users] segmentation fault with grompp

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 9 23:24:42 CET 2010

Gard Nelson wrote:
> Hey everyone,
> I wrote a few days ago about a segmentation fault I'm getting from 
> grompp when I try to set up a membrane protein system.  Grompp opens the 
> ff_dum.itp file and then the core dumps immediately.  This happens on 
> two different machines, both of which are running gromacs 4.0.5. 
> I just downloaded lipid.itp, popc128a.pdb and popc.itp fresh from 
> Tieleman's website, made a topology file and tried running grompp on 
> it.  I still get the same segmentation fault.  However, when I run the 
> same files through grompp from gromacs 3.3, it works fine.  Has anyone 
> else seen this problem, or is it just me?  What can I do to find and fix 
> the problem? 

Can you post the topology you made?  What about ff_dum.itp?  I believe Mark 
asked about its integrity some time ago.  I've certainly processed a number of 
membrane and membrane-protein systems under Gromacs 4.0.x, so I don't think 
there's anything inherently wrong with grompp.


> Thanks
> Gard Nelson


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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