simulation.rst



Simulation
The simulation finally connects a :class:`Topology` with an
:class:`ost.mol.EntityHandle`. While applying minimization or
MD tasks, the current positions of the simulation object can be
mapped back to the attached structure at any time.
first constructor, that takes an :class:`ost.mol.EntityHandle` as an input
and automatically constructs an internal :class:`Topology` according
to the provided settings. Be aware, that the entity will be altered
depending on hydrogen/termini definitions in the :class:`Forcefield` attached
to the settings


param entity:
:class:`ost.mol.EntityHandle` from which a default
:class:`Topology` will be created according to the
settings


param settings:
:class:`Settings` to control the parametrization of
the :class:`Simulation` and the buildup of the
internal :class:`Topology`


raises:
:class:`RuntimeError` when construction of
:class:`Topology` fails


second constructor, that takes a :class:`Topology` and a consistent
:class:`ost.mol.EntityHandle` as an input.


param topology:
:class:`Topology` to initialize the :class:`Simulation`


param entity:
:class:`ost.mol.EntityHandle` that is consistent with
the provided topology


param settings:
:class:`Settings` to control the parametrization of
the :class:`Simulation`


raises:
:class:`RuntimeException` when number of atoms in
entity is not equal the number of particles
in topology