About OOPSE OOPSE News Features Download CVS Mailing Lists Documentation Authors Funding Results	The Empirical Energy Functions Like many simulation packages, OOPSE splits the potential energy into the short-ranged (bonded) portion and a long-range (non-bonded) potential, $$V = V_{\mathrm{short-range}} + V_{\mathrm{long-range}}.$$ (3.1) The short-ranged portion includes the explicit bonds, bends, and torsions which have been defined in the meta-data file for the molecules which are present in the simulation. The functional forms and parameters for these interactions are defined by the force field which is chosen. Calculating the long-range (non-bonded) potential involves a sum over all pairs of atoms (except for those atoms which are involved in a bond, bend, or torsion with each other). If done poorly, calculating the the long-range interactions for $N$ atoms would involve $N(N-1)/2$ evaluations of atomic distances. To reduce the number of distance evaluations between pairs of atoms, OOPSE uses a switched cutoff with Verlet neighbor lists.[12] It is well known that neutral groups which contain charges will exhibit pathological forces unless the cutoff is applied to the neutral groups evenly instead of to the individual atoms.[14] OOPSE allows users to specify cutoff groups which may contain an arbitrary number of atoms in the molecule. Atoms in a cutoff group are treated as a single unit for the evaluation of the switching function: $$V_{\mathrm{long-range}} = \sum_{a} \sum_{b>a} s(r_{ab}) \sum_{i \in a} \sum_{j \in b} V_{ij}(r_{ij}),$$ (3.2) where $r_{ab}$ is the distance between the centers of mass of the two cutoff groups ($a$ and $b$ ). The sums over $a$ and $b$ are over the cutoff groups that are present in the simulation. Atoms which are not explicitly defined as members of a cutoffGroup are treated as a group consisting of only one atom. The switching function, $s(r)$ is the standard cubic switching function, $$S(r) = \begin{cases}1 & \text{if $r \le r_{\text{sw}}$},\\ \frac{... ...}} < r \le r_{\text{cut}}$}, \\ 0 & \text{if $r > r_{\text{cut}}$.} \end{cases}$$ (3.3) Here, $r_{\text{sw}}$ is the switchingRadius, or the distance beyond which interactions are reduced, and $r_{\text{cut}}$ is the cutoffRadius, or the distance at which interactions are truncated. Users of OOPSE do not need to specify the cutoffRadius or switchingRadius. In simulations containing only Lennard-Jones atoms, the cutoff radius has a default value of $2.5\sigma_{ii}$ , where $\sigma_{ii}$ is the largest Lennard-Jones length parameter present in the simulation. In simulations containing charged or dipolar atoms, the default cutoff radius is $15$   Å . The switchingRadius is set to a default value of 95% of the cutoffRadius. In the special case of a simulation containing only Lennard-Jones atoms, the default switching radius takes the same value as the cutoff radius, and OOPSE will use a shifted potential to remove discontinuities in the potential at the cutoff. Both radii may be specified in the meta-data file. Force fields can be added to OOPSE, although it comes with a few simple examples (Lennard-Jones, DUFF, WATER, and EAM) which are explained in the following sections.
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	Updated on January 16, 2006