[gmx-users] Energy analysis by mdrun -rerun

Shang-Te Danny Hsu hsu at panda.chem.uu.nl
Mon Jun 2 16:23:01 CEST 2003

Hi there,

I am re-running the simulations with mdrun -rerun option and subsets of
groups. Errors occur when the protein molecule is moving out of the
rectangular periodic box. It then outputs all the broken molecule PDB files
due to the error of LINCS constraints.

I tried to restore the molecule in to one piece by trjconv -pbc nojump (or
whole) but it did not work. For one case the energy file *.edr went okay but
other cases gave huge Coul/JL protein-SOL energy values (> 1e+09 KJ/mol). Is
there anyway I can fix this problem?

Shang-Te Danny Hsu [Ph.D. student]
NMR Spectroscopy, Bijvoet Center
Universteit Utrecht
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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