[gmx-users] mdrun segmentation fault

Justin A. Lemkul jalemkul at vt.edu
Thu May 20 23:30:23 CEST 2010

Sikandar Mashayak wrote:
> Hi
> I have gromacs input files for md simulation, with these set up files 
> (*.mdp,*.top,*.itp *.gro), I can successfully run grompp and mdrun on 
> one machine, but when I move it to other machine, I get segmentation 
> fault when I do mdrun. Both the machines have exactly same types of 
> installation of gromacs 4.0.7 . Also, I can run water tutorials 
> successfully on both the machines.
> So what could be the source of segmentation fault?

MD is chaotic, so you may not get the same result every time you run a 
simulation.  Since you've not said how quickly the seg fault occurs it is 
exceptionally hard to diagnose.  Generally, seg faults with mdrun occur because 
the system crashes from an instability.  Without substantially more information 
(system contents, .mdp settings, relevant log file output, etc) there is not 
much more to suggest.


> thanks
> sikandar


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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