About OOPSE OOPSE News Features Download CVS Mailing Lists Documentation Authors Funding Results	Dipolar Unified-Atom Force Field The dipolar unified-atom force field (DUFF) was developed to simulate lipid bilayers. These types of simulations require a model capable of forming bilayers, while still being sufficiently computationally efficient to allow large systems ($\sim$ 100's of phospholipids, $\sim$ 1000's of waters) to be simulated for long times ($\sim$ 10's of nanoseconds). With this goal in mind, DUFF has no point charges. Charge-neutral distributions are replaced with dipoles, while most atoms and groups of atoms are reduced to Lennard-Jones interaction sites. This simplification reduces the length scale of long range interactions from $\frac{1}{r}$ to $\frac{1}{r^3}$ , removing the need for the computationally expensive Ewald sum. Instead, Verlet neighbor-lists and cutoff radii are used for the dipolar interactions, and, if desired, a reaction field may be added to mimic longer range interactions. As an example, lipid head-groups in DUFF are represented as point dipole interaction sites. Placing a dipole at the head group's center of mass mimics the charge separation found in common phospholipid head groups such as phosphatidylcholine.[15] Additionally, a large Lennard-Jones site is located at the pseudoatom's center of mass. The model is illustrated by the red atom in Fig. 3.1. The water model we use to complement the dipoles of the lipids is a reparameterization[16] of the soft sticky dipole (SSD) model of Ichiye et al.[17] Figure 3.1: A representation of the lipid model. $\phi$ is the torsion angle, $\theta$ is the bend angle, and $\mu$ is the dipole moment of the head group. A set of scalable parameters has been used to model the alkyl groups with Lennard-Jones sites. For this, parameters from the TraPPE force field of Siepmann et al.[18] have been utilized. TraPPE is a unified-atom representation of n-alkanes which is parametrized against phase equilibria using Gibbs ensemble Monte Carlo simulation techniques.[18] One of the advantages of TraPPE is that it generalizes the types of atoms in an alkyl chain to keep the number of pseudoatoms to a minimum; thus, the parameters for a unified atom such as CH$_2$ do not change depending on what species are bonded to it. As is required by TraPPE, DUFF also constrains all bonds to be of fixed length. Typically, bond vibrations are the fastest motions in a molecular dynamic simulation. With these vibrations present, small time steps between force evaluations must be used to ensure adequate energy conservation in the bond degrees of freedom. By constraining the bond lengths, larger time steps may be used when integrating the equations of motion. A simulation using DUFF is illustrated in Scheme 3.2.
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