[gmx-users] Re: RMSF error when fitting to average structure
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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