Sounds like your system may be blowing up somehow, but without more
information (MD input file, example of the problematic output, etc) we
can only guess at what's happening. You can try to use the cpptraj
'check' command to look for unusual bond lengths although this could
be time consuming depending on the size of your system. The openmp
version will run 'check' much faster.
-Dan
On Thu, Mar 9, 2017 at 5:51 AM, Beale, John <John.Beale.stlcop.edu> wrote:
> Hello,
>
> I am trying to run an accelerated molecular dynamics experiment on a 441-residue protein. The simulation runs just fine until it reaches about 2 million steps, and then the out file shows that the BOND and EAMD_BOOST energy fields contain strings of asterisks instead of the energy values for those terms. Can someone tell me what could be causing this and how I might proceed to correct the problem?
>
> John
>
>
> John M. Beale, Jr.
> John M. Beale, Jr., Ph.D.
> Professor of Medicinal Chemistry and Pharmacognosy
> Saint Louis College of Pharmacy
> 4588 Parkview Place
> Saint Louis, Missouri 63110-1088
> Office: 314-446-8461
> Cell: 314-315-0409
> FAX: 314-446-8460
> John.Beale.stlcop.edu<mailto:John.Beale.stlcop.edu>
>
> _______________________________________________
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Mar 09 2017 - 06:00:03 PST
