[gmx-users] Re: RMSF error when fitting to average structure

Justin Lemkul jalemkul at vt.edu
Thu Aug 16 22:05:13 CEST 2012

On 8/16/12 3:54 PM, tdgrant1 wrote:
> Oh okay, thanks.  I didn't realize warnings were just that, only warnings and
> didn't stop the program.  The program did not finish however, and the
> problem was a Segmentation Fault.  The output literally was:
> Select a group: 0
> Selected 0: 'System'
> Reading frame       0 time    0.000
> WARNING: if there are broken molecules in the trajectory file,
>           they can not be made whole without a run input file
> Segmentation fault
> Could this be related to the input file, or do you think this is something
> else entirely?

Depending on how many atoms are in the entire system (is it a fully solvated 
protein, anything else?) then you probably ran out of memory.  These analyses 
are normally performed only on the solute of interest or a subset of those atoms 
(like a protein backbone).



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


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