About OOPSE OOPSE News Features Download CVS Mailing Lists Documentation Authors Funding Results	Concepts & Files A simulation in OOPSE is built using a few fundamental conceptual building blocks most of which are chemically intuitive. The basic unit of a simulation is an atom. The parameters describing an atom have been generalized to make it as flexible as possible; this means that in addition to translational degrees of freedom, Atoms may also have orientational degrees of freedom. The fundamental (static) properties of atoms are defined by the forceField chosen for the simulation. The atomic properties specified by a forceField might include (but are not limited to) charge, $\sigma$ and $\epsilon$ values for Lennard-Jones interactions, the strength of the dipole moment ($\mu$ ), the mass, and the moments of inertia. Other more complicated properties of atoms might also be specified by the forceField. Atoms can be grouped together in many ways. A rigidBody contains atoms that exert no forces on one another and which move as a single rigid unit. A cutoffGroup may contain atoms which function together as a (rigid or non-rigid) unit for potential energy calculations, $$V_{ab} = s(r_{ab}) \sum_{i \in a} \sum_{j \in b} V_{ij}(r_{ij})$$ (2.1) Here, $a$ and $b$ are two cutoffGroups containing multiple atoms ( $a = \left\{i\right\}$ and $b = \left\{j\right\}$ ). $s(r_{ab})$ is a generalized switching function which insures that the atoms in the two cutoffGroups are treated identically as the two groups enter or leave an interaction region. Atoms may also be grouped in more traditional ways into bonds, bends, and torsions. These groupings allow the correct choice of interaction parameters for short-range interactions to be chosen from the definitions in the forceField. All of these groups of atoms are brought together in the molecule, which is the fundamental structure for setting up and OOPSE simulation. Molecules contain lists of atoms followed by listings of the other atomic groupings (bonds, bends, torsions, rigidBodies, and cutoffGroups) which relate the atoms to one another. Simulations often involve heterogeneous collections of molecules. To specify a mixture of molecule types, OOPSE uses components. Even simulations containing only one type of molecule must specify a single component. Starting a simulation requires two types of information: meta-data, which describes the types of objects present in the simulation, and configuration information, which describes the initial state of these objects. The meta-data is given to OOPSE using a C-based syntax that is parsed at the beginning of the simulation. Configuration information is specified using an extended XYZ file format. Both the meta-data and configuration file formats are described in the following sections.
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	Updated on January 16, 2006