| 284 |
|
In the interest of computational efficiency, the default solvent used |
| 285 |
|
by {\sc oopse} is the extended Soft Sticky Dipole (SSD/E) water |
| 286 |
|
model.\cite{Gezelter04} The original SSD was developed by Ichiye |
| 287 |
< |
\emph{et al.}\cite{Ichiye96} as a modified form of the hard-sphere |
| 287 |
> |
\emph{et al.}\cite{liu96:new_model} as a modified form of the hard-sphere |
| 288 |
|
water model proposed by Bratko, Blum, and |
| 289 |
|
Luzar.\cite{Bratko85,Bratko95} It consists of a single point dipole |
| 290 |
|
with a Lennard-Jones core and a sticky potential that directs the |
| 337 |
|
while $w^\prime$ is a purely empirical function. A more detailed |
| 338 |
|
description of the functional parts and variables in this potential |
| 339 |
|
can be found in the original SSD |
| 340 |
< |
articles.\cite{Ichiye96,Ichiye96b,Ichiye99,Ichiye03} |
| 340 |
> |
articles.\cite{liu96:new_model,liu96:monte_carlo,chandra99:ssd_md,Ichiye03} |
| 341 |
|
|
| 342 |
|
Since SSD is a single-point {\it dipolar} model, the force |
| 343 |
|
calculations are simplified significantly relative to the standard |
| 344 |
|
{\it charged} multi-point models. In the original Monte Carlo |
| 345 |
|
simulations using this model, Ichiye {\it et al.} reported that using |
| 346 |
|
SSD decreased computer time by a factor of 6-7 compared to other |
| 347 |
< |
models.\cite{Ichiye96} What is most impressive is that these savings |
| 347 |
> |
models.\cite{liu96:new_model} What is most impressive is that these savings |
| 348 |
|
did not come at the expense of accurate depiction of the liquid state |
| 349 |
|
properties. Indeed, SSD maintains reasonable agreement with the Soper |
| 350 |
|
diffraction data for the structural features of liquid |
| 351 |
< |
water.\cite{Soper86,Ichiye96} Additionally, the dynamical properties |
| 351 |
> |
water.\cite{Soper86,liu96:new_model} Additionally, the dynamical properties |
| 352 |
|
exhibited by SSD agree with experiment better than those of more |
| 353 |
|
computationally expensive models (like TIP3P and |
| 354 |
< |
SPC/E).\cite{Ichiye99} The combination of speed and accurate depiction |
| 354 |
> |
SPC/E).\cite{chandra99:ssd_md} The combination of speed and accurate depiction |
| 355 |
|
of solvent properties makes SSD a very attractive model for the |
| 356 |
|
simulation of large scale biochemical simulations. |
| 357 |
|
|
