[gmx-users] mdrun segmentation fault

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 11 15:41:13 CEST 2011

shivangi nangia wrote:
> Hello gmx users,
> My system for NVT equilbration runs into segmentation fault as soon as I 
> try to run it.
> It does not give any warning or hint of what might be going wrong.
> Since I am a new user I am having difficulty exploring the plausible 
> reasons.
> System: Protein( polyhistidine), 20  2,5-dihydroxybenzoic acid anions, 
> 1:1 water: methanol (~3000 molecules of each) in 8 nm cube
> I had had EM of the system using steepest decent. Outcome:
> Steepest Descents converged to machine precision in 15 steps, but did 
> not reach the requested Fmax < 1000.
> Potential Energy  =  1.5354981e+19
> Maximum force     =            inf on atom 651
> Norm of force     =            inf

You were already told that this is the source of your problem and any procedure 
is destined to fail.  What's more, you were given hints on how to solve your issue:




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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