About OOPSE OOPSE News Features Download CVS Mailing Lists Documentation Authors Funding Results	The DUFF Water Models: SSD/E and SSD/RF In the interest of computational efficiency, the default solvent used by OOPSE is the extended Soft Sticky Dipole (SSD/E) water model.[16] The original SSD was developed by Ichiye et al.[17] as a modified form of the hard-sphere water model proposed by Bratko, Blum, and Luzar.[19,20] It consists of a single point dipole with a Lennard-Jones core and a sticky potential that directs the particles to assume the proper hydrogen bond orientation in the first solvation shell. Thus, the interaction between two SSD water molecules i and j is given by the potential $$V_{ij} = V_{ij}^{LJ} (r_{ij})\ + V_{ij}^{dp} (\mathbf{r}_{ij},\bo... ...)\ + V_{ij}^{sp} (\mathbf{r}_{ij},\boldsymbol{\Omega}_i,\boldsymbol{\Omega}_j),$$ (3.15) where the $\mathbf{r}_{ij}$ is the position vector between molecules i and j with magnitude equal to the distance $r_{ij}$ , and $\boldsymbol{\Omega}_i$ and $\boldsymbol{\Omega}_j$ represent the orientations of the respective molecules. The Lennard-Jones and dipole parts of the potential are given by equations 3.4 and 3.14 respectively. The sticky part is described by the following, $$u_{ij}^{sp}(\mathbf{r}_{ij},\boldsymbol{\Omega}_i,\boldsymbol{\Om... ...{ij})w^\prime(\mathbf{r}_{ij}, \boldsymbol{\Omega}_i,\boldsymbol{\Omega}_j)]\ ,$$ (3.16) where $\nu_0$ is a strength parameter for the sticky potential, and $s$ and $s^\prime$ are cubic switching functions which turn off the sticky interaction beyond the first solvation shell. The $w$ function can be thought of as an attractive potential with tetrahedral geometry: $$w({\bf r}_{ij},{\bf\Omega}_i,{\bf\Omega}_j)= \sin\theta_{ij}\sin2\theta_{ij}\cos2\phi_{ij},$$ (3.17) while the $w^\prime$ function counters the normal aligned and anti-aligned structures favored by point dipoles: $$w^\prime({\bf r}_{ij},{\bf\Omega}_i,{\bf\Omega}_j)= (\cos\theta_{ij}-0.6)^2(\cos\theta_{ij}+0.8)^2-w^0,$$ (3.18) It should be noted that $w$ is proportional to the sum of the $Y_3^2$ and $Y_3^{-2}$ spherical harmonics (a linear combination which enhances the tetrahedral geometry for hydrogen bonded structures), while $w^\prime$ is a purely empirical function. A more detailed description of the functional parts and variables in this potential can be found in the original SSD articles.[17,21,22,23] Figure 3.2: Coordinates for the interaction between two SSD/E water molecules. $\theta_{ij}$ is the angle that $r_{ij}$ makes with the $\hat{z}$ vector in the body-fixed frame for molecule $i$ . The $\hat{z}$ vector bisects the HOH angle in each water molecule. Since SSD/E is a single-point dipolar model, the force calculations are simplified significantly relative to the standard charged multi-point models. In the original Monte Carlo simulations using this model, Ichiye et al. reported that using SSD decreased computer time by a factor of 6-7 compared to other models.[17] What is most impressive is that these savings did not come at the expense of accurate depiction of the liquid state properties. Indeed, SSD/E maintains reasonable agreement with the Head-Gordon diffraction data for the structural features of liquid water.[24,17] Additionally, the dynamical properties exhibited by SSD/E agree with experiment better than those of more computationally expensive models (like TIP3P and SPC/E).[22] The combination of speed and accurate depiction of solvent properties makes SSD/E a very attractive model for the simulation of large scale biochemical simulations. Recent constant pressure simulations revealed issues in the original SSD model that led to lower than expected densities at all target pressures.[23,16] The default model in OOPSE is therefore SSD/E, a density corrected derivative of SSD that exhibits improved liquid structure and transport behavior. If the use of a reaction field long-range interaction correction is desired, it is recommended that the parameters be modified to those of the SSD/RF model (an SSD variant parameterized for reaction field). These solvent parameters are listed and can be easily modified in the DUFF force field file (DUFF.frc). A table of the parameter values and the drawbacks and benefits of the different density corrected SSD models can be found in reference [16].
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	Updated on January 16, 2006