[gmx-users] Energy analysis by mdrun -rerun
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jun 3 13:21:01 CEST 2003
On Tue, 2003-06-03 at 10:51, Shang-Te Danny Hsu wrote:
> > Shang-Te Danny Hsu wrote:
> >> 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.
> > Try turning off constraints in the .tpr file you use for the '-rerun'.
> > (e.g. constraints = none in your .mdp file)
> Hi Anton,
> Thank, but...
> It did not work! I have no idea where else to look for
are you sure your trr/xtc is correct? Did you use shuffling to make it?
Have you check energy terms (e.g. bonds/angles/impropers) to see whether
they have reasonable values?
It seems most like a tpr/xtc mismatch....
Dr. David van der Spoel, Dept. of Cell & Mol. Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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