About OOPSE OOPSE News Features Download CVS Mailing Lists Documentation Authors Funding Results	Generation of Initial Coordinates As was stated in Sec. 2.4, an initial coordinate file is needed to provide the starting coordinates for a simulation. Since each simulation is different, system creation is left to the end user; however, we have included a few sample programs which make some specialized structures. The .in file must list the integrable objects in the correct order. The ordering of the integrable objects relies on the ordering of molecules within the meta-data file. OOPSE expects the order to comply with the following guidelines: All of the molecules of the first declared component are given before proceeding to the molecules of the second component, and so on for all subsequently declared components. The ordering of the atoms for each molecule follows the order declared in the molecule's declaration within the model file. Only atoms which are not members of a rigidBody are included. Rigid Body coordinates for a molecule are listed immediately after the the other atoms in a molecule. Some molecules may be entirely rigid, in which case, only the rigid body coordinates are given. An example is given in the meta-data file in Scheme 2.6 which results in the .in file shown in Scheme 2.7.
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