| 233 |
|
Where $r_{ij}$ is the distance between particles $i$ and $j$, |
| 234 |
|
$\sigma_{ij}$ scales the length of the interaction, and |
| 235 |
|
$\epsilon_{ij}$ scales the well depth of the potential. Scheme |
| 236 |
< |
\ref{sch:LJFF} gives and example \texttt{.bass} file that |
| 236 |
> |
\ref{sch:LJFF} gives an example \texttt{.bass} file that |
| 237 |
|
sets up a system of 108 Ar particles to be simulated using the |
| 238 |
|
Lennard-Jones force field. |
| 239 |
|
|
| 264 |
|
the energy value at $r_{\text{cut}}$ is subtracted from the |
| 265 |
|
potential. This causes the potential to go to zero smoothly at the |
| 266 |
|
cut-off radius, and preserves conservation of energy in integrating |
| 267 |
< |
the equations of motion. |
| 267 |
> |
the equations of motion. There still remains a discontinuity in the derivative (the forces), however, this does not significantly affect the dynamics. |
| 268 |
|
|
| 269 |
|
Interactions between dissimilar particles requires the generation of |
| 270 |
|
cross term parameters for $\sigma$ and $\epsilon$. These are |
| 381 |
|
Here $V_{\text{bend}}$ is the bend potential for all 1, 3 bonded pairs |
| 382 |
|
within the molecule $I$, and $V_{\text{torsion}}$ is the torsion potential |
| 383 |
|
for all 1, 4 bonded pairs. The pairwise portions of the internal |
| 384 |
< |
potential are excluded for pairs that are closer than three bonds, |
| 385 |
< |
i.e.~atom pairs farther away than a torsion are included in the |
| 386 |
< |
pair-wise loop. |
| 384 |
> |
potential are excluded for atom pairs that are involved in the same bond, bend, or torsion. All other atom pairs within the molecule are subject to the LJ pair potential. |
| 385 |
|
|
| 386 |
|
|
| 387 |
|
The bend potential of a molecule is represented by the following function: |
| 571 |
|
exhibits improved liquid structure and transport behavior. If the use |
| 572 |
|
of a reaction field long-range interaction correction is desired, it |
| 573 |
|
is recommended that the parameters be modified to those of the SSD/RF |
| 574 |
< |
model. Solvent parameters can be easily modified in an accompanying |
| 574 |
> |
model (an SSD variant parameterized for reaction field). Solvent parameters can be easily modified in an accompanying |
| 575 |
|
\texttt{.bass} file as illustrated in the scheme below. A table of the |
| 576 |
|
parameter values and the drawbacks and benefits of the different |
| 577 |
|
density corrected SSD models can be found in |
| 1656 |
|
oopse}, we have implemented the {\sc rattle} algorithm of |
| 1657 |
|
Andersen.\cite{andersen83} The algorithm is a velocity verlet |
| 1658 |
|
formulation of the {\sc shake} method\cite{ryckaert77} of iteratively |
| 1659 |
< |
solving the Lagrange multipliers of constraint. The system of lagrange |
| 1659 |
> |
solving the Lagrange multipliers of constraint. The system of Lagrange |
| 1660 |
|
multipliers allows one to reformulate the equations of motion with |
| 1661 |
|
explicit constraint forces.\cite{fowles99:lagrange} |
| 1662 |
|
|
| 2229 |
|
\texttt{dynamicProps} will calculate all of the time correlation frame |
| 2230 |
|
pairs within the block. After in-block correlations are complete, a |
| 2231 |
|
second block of the trajectory is read, and the cross correlations are |
| 2232 |
< |
calculated between the two blocks. this second block is then freed and |
| 2232 |
> |
calculated between the two blocks. This second block is then freed and |
| 2233 |
|
then incremented and the process repeated until the end of the |
| 2234 |
|
trajectory. Once the end is reached, the first block is freed then |
| 2235 |
|
incremented, and the again the internal time correlations are |
| 2259 |
|
z-constraint method. |
| 2260 |
|
|
| 2261 |
|
These features are all brought together in a single open-source |
| 2262 |
< |
program. Allowing researchers to not only benefit from |
| 2262 |
> |
program. This allows researchers to not only benefit from |
| 2263 |
|
{\sc oopse}, but also contribute to {\sc oopse}'s development as |
| 2264 |
|
well. |
| 2265 |
|
|
