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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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