565 |
|
made of 2266 small identical beads with size of 0.3 \AA on the |
566 |
|
surface. Applying the procedure described in |
567 |
|
Sec.~\ref{introEquation:ResistanceTensorArbitraryOrigin}, we |
568 |
< |
identified the center of resistance at $(0\AA, 0.7482\AA, |
569 |
< |
-0.1988\AA)$, as well as the resistance tensor, |
568 |
> |
identified the center of resistance at $(0 \AA, 0.7482 \AA, |
569 |
> |
-0.1988 \AA)$, as well as the resistance tensor, |
570 |
|
\[ |
571 |
|
\left( {\begin{array}{*{20}c} |
572 |
|
0.9261 & 0 & 0&0&0.08585&0.2057\\ |
593 |
|
However, because of the stochastic nature, simulation using Langevin |
594 |
|
dynamics was shown to decay slightly faster than MD. In order to |
595 |
|
study the rotational motion of the molecules, we also calculated the |
596 |
< |
auto- correlation function of the principle axis of the second GB |
596 |
> |
auto-correlation function of the principle axis of the second GB |
597 |
|
particle, $u$. The discrepancy shown in Fig.~\ref{langevin:uacf} was |
598 |
|
probably due to the reason that the viscosity using in the |
599 |
|
simulations only partially preserved the dynamics of the system. |
617 |
|
\centering |
618 |
|
\includegraphics[width=\linewidth]{vacf.eps} |
619 |
|
\caption[Plots of Velocity Auto-correlation Functions]{Velocity |
620 |
< |
auto-correlation functions of NVE (explicit solvent) in blue) and |
620 |
> |
auto-correlation functions of NVE (explicit solvent) in blue and |
621 |
|
Langevin dynamics (implicit solvent) in red.} \label{langevin:vacf} |
622 |
|
\end{figure} |
623 |
|
|