[MMTK] Solvation example

Konrad Hinsen hinsen at cnrs-orleans.fr
Tue Oct 21 17:54:52 CEST 2003

On Thursday 16 October 2003 10:01, Michiel Jan Laurens de Hoon wrote:

> Thank you again for your answer. This problem occurs with the
> solvation.py that is in Examples/MolecularDynamics; I only added
> universe.view() at the end. I looked some more to find out where
> universe.view() first causes problems. This function works correctly
> until the thermostat is set in line 71:

That is due to a small bug, which will be fixed in the next release. For those 
who want an immediate fix, replace the method "_changed" in the class 
"Universe" (file Universe.py) by the following:

    def _changed(self, system_size_changed):
	self._evaluator = {}
        self._bond_database = None
	self._version = self._version + 1
        if system_size_changed:
            self._configuration = None
            self._masses = None
            self._atom_properties = {}
            self._atoms = None
            self._np = None
            self._bond_pairs = None
            if self._configuration is not None:
                self._configuration.version = self._version
            if self._masses is not None:
                self._masses.version = self._version

Konrad Hinsen                            | E-Mail: hinsen at cnrs-orleans.fr
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-
Rue Charles Sadron                       | Fax:  +33-
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