[gmx-users] Energy analysis by mdrun -rerun

[Anton Feenstra]

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)


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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