About OOPSE OOPSE News Features Download CVS Mailing Lists Documentation Authors Funding Results	Creating a Metadata File The actual creation of a metadata file requires several key components. The first part of the file needs to be the declaration of all of the molecule prototypes used in the simulation. This is typically done through included meta-data files. Only the molecules actually present in the simulation need to be declared; however, OOPSE allows for the declaration of more molecules than are needed. This gives the user the ability to build up a library of commonly used molecules into a single include file. Once all prototypes are declared, the ordering of the rest of the script is less stringent. The molecular composition of the simulation is specified with component statements. Each different type of molecule present in the simulation is considered a separate component. The number of components must be declared before the first component block statement (an example is shown in Sch. 2.3). The component blocks tell OOPSE the number of molecules that will be in the simulation, and the order in which the components blocks are declared sets the ordering of the real atoms in the configuration file as well as in the output files. The remainder of the script then sets the various simulation parameters for the system of interest. The required set of parameters that must be present in all simulations is given in Table 2.1. Since the user can use OOPSE to perform energy minimizations as well as molecular dynamics simulations, one of the minimizer or ensemble keywords must be present. The ensemble keyword is responsible for selecting the integration method used for the calculation of the equations of motion. An in depth discussion of the various methods available in OOPSE can be found in Sec. 4. The minimizer keyword selects which minimization method to use, and more details on the choices of minimizer parameters can be found in Sec. 5. The forceField statement is important for the selection of which forces will be used in the course of the simulation. OOPSE supports several force fields, as outlined in Sec. 3. The force fields are interchangeable between simulations, with the only requirement being that all atoms needed by the simulation are defined within the selected force field. For molecular dynamics simulations, the time step between force evaluations is set with the dt parameter, and runTime will set the time length of the simulation. Note, that runTime is an absolute time, meaning if the simulation is started at t = 10.0 ns with a runTime of 25.0 ns, the simulation will only run for an additional 15.0 ns. For energy minimizations, it is not necessary to specify dt or runTime. The final required parameter is the initialConfig statement. This will set the initial coordinates for the system, as well as the initial time if the useInitalTime flag is set to true. The format of the file specified in initialConfig, is given in Sec. 2.4. Additional parameters are summarized in Table 2.2. It is important to note the fundamental units in all files which are read and written by OOPSE. Energies are in kcal mol$^{-1}$ , distances are in Å , times are in fs , translational velocities are in Å fs$^{-1}$ , and masses are in amu . Orientational degrees of freedom are described using quaternions (unitless, but $q_w^2 + q_x^2 + q_y^2 + q_z^2 = 1$ ), body-fixed angular momenta ( amu Å$^{2}$   radians fs$^{-1}$ ), and body-fixed moments of inertia ( amu Å$^{2}$ ). Table 2.1: Meta-data Keywords: Required Parameters Table 2.2: Meta-data Keywords: General Parameters
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