[gmx-users] energy analysis by [rerun]

Shang-Te Danny Hsu hsu at nmr.chem.uu.nl
Fri Dec 14 12:00:18 CET 2001

Dear listers,

I had some problems with the [ mdrun -rerun ] protocol for the energy 
analysis. I've been analysis for several trajctories and most of them 
were okay. Yet, some stopped with the following message:

    2206   2207   34.0    0.1533   0.1889      0.1530
    2212   2213   32.8    0.1228   0.1557      0.1230
    2212   2214   32.2    0.1330   0.1692      0.1330
Wrote pdb files with previous and current coordinates
Fatal error: Bond deviates more than half its own length

However, the *.xtc files were complete trajactory files without any 
crash in between. Isn't it just to recalculate the energy in different 
groups defined by another index file *.ndx? If the original analysis was 
okay, why did this error message pop up?

Does [ mdrun -rerun ] generate another trajctory?

Shang-Te Danny HSU
Department of NMR Spectroscopy
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht, the Netherlands
phone: +31-30-2539931 | fax: +31-30-2537623
e-mail: hsu at nmr.chem.uu.nl

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