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\chapter{\label{chapt:methodology}METHODOLOGY} |
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\section{\label{methodSection:rigidBodyIntegrators}Integrators for Rigid Body Motion in Molecular Dynamics} |
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In order to mimic the experiments, which are usually performed under |
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constant temperature and/or pressure, extended Hamiltonian system |
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methods have been developed to generate statistical ensembles, such |
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as canonical ensemble and isobaric-isothermal ensemble \textit{etc}. |
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In addition to the standard ensemble, specific ensembles have been |
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developed to account for the anisotropy between the lateral and |
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normal directions of membranes. The $NPAT$ ensemble, in which the |
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normal pressure and the lateral surface area of the membrane are |
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kept constant, and the $NP\gamma T$ ensemble, in which the normal |
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pressure and the lateral surface tension are kept constant were |
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proposed to address this issue. |
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Integration schemes for rotational motion of the rigid molecules in |
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microcanonical ensemble have been extensively studied in the last |
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two decades. Matubayasi and Nakahara developed a time-reversible |
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integrator for rigid bodies in quaternion representation. Although |
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it is not symplectic, this integrator still demonstrates a better |
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long-time energy conservation than traditional methods because of |
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the time-reversible nature. Extending Trotter-Suzuki to general |
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system with a flat phase space, Miller and his colleagues devised an |
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novel symplectic, time-reversible and volume-preserving integrator |
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in quaternion representation, which was shown to be superior to the |
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time-reversible integrator of Matubayasi and Nakahara. However, all |
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of the integrators in quaternion representation suffer from the |
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computational penalty of constructing a rotation matrix from |
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quaternions to evolve coordinates and velocities at every time step. |
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An alternative integration scheme utilizing rotation matrix directly |
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proposed by Dullweber, Leimkuhler and McLachlan (DLM) also preserved |
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the same structural properties of the Hamiltonian flow. In this |
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section, the integration scheme of DLM method will be reviewed and |
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extended to other ensembles. |
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\subsection{\label{methodSection:DLM}Integrating the Equations of Motion: the |
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DLM method} |
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The DLM method uses a Trotter factorization of the orientational |
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propagator. This has three effects: |
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\begin{enumerate} |
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\item the integrator is area-preserving in phase space (i.e. it is |
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{\it symplectic}), |
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\item the integrator is time-{\it reversible}, making it suitable for Hybrid |
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Monte Carlo applications, and |
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\item the error for a single time step is of order $\mathcal{O}\left(h^4\right)$ |
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for timesteps of length $h$. |
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\end{enumerate} |
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The integration of the equations of motion is carried out in a |
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velocity-Verlet style 2-part algorithm, where $h= \delta t$: |
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{\tt moveA:} |
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\begin{align*} |
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{\bf v}\left(t + h / 2\right) &\leftarrow {\bf v}(t) |
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+ \frac{h}{2} \left( {\bf f}(t) / m \right), \\ |
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% |
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{\bf r}(t + h) &\leftarrow {\bf r}(t) |
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+ h {\bf v}\left(t + h / 2 \right), \\ |
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% |
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{\bf j}\left(t + h / 2 \right) &\leftarrow {\bf j}(t) |
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+ \frac{h}{2} {\bf \tau}^b(t), \\ |
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% |
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\mathsf{A}(t + h) &\leftarrow \mathrm{rotate}\left( h {\bf j} |
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(t + h / 2) \cdot \overleftrightarrow{\mathsf{I}}^{-1} \right). |
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\end{align*} |
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In this context, the $\mathrm{rotate}$ function is the reversible |
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product of the three body-fixed rotations, |
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\begin{equation} |
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\mathrm{rotate}({\bf a}) = \mathsf{G}_x(a_x / 2) \cdot |
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\mathsf{G}_y(a_y / 2) \cdot \mathsf{G}_z(a_z) \cdot \mathsf{G}_y(a_y |
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/ 2) \cdot \mathsf{G}_x(a_x /2), |
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\end{equation} |
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where each rotational propagator, $\mathsf{G}_\alpha(\theta)$, |
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rotates both the rotation matrix ($\mathsf{A}$) and the body-fixed |
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angular momentum (${\bf j}$) by an angle $\theta$ around body-fixed |
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axis $\alpha$, |
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\begin{equation} |
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\mathsf{G}_\alpha( \theta ) = \left\{ |
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\begin{array}{lcl} |
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\mathsf{A}(t) & \leftarrow & \mathsf{A}(0) \cdot \mathsf{R}_\alpha(\theta)^T, \\ |
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{\bf j}(t) & \leftarrow & \mathsf{R}_\alpha(\theta) \cdot {\bf |
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j}(0). |
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\end{array} |
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\right. |
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\end{equation} |
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$\mathsf{R}_\alpha$ is a quadratic approximation to the single-axis |
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rotation matrix. For example, in the small-angle limit, the |
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rotation matrix around the body-fixed x-axis can be approximated as |
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\begin{equation} |
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\mathsf{R}_x(\theta) \approx \left( |
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\begin{array}{ccc} |
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1 & 0 & 0 \\ |
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0 & \frac{1-\theta^2 / 4}{1 + \theta^2 / 4} & -\frac{\theta}{1+ |
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\theta^2 / 4} \\ |
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0 & \frac{\theta}{1+ \theta^2 / 4} & \frac{1-\theta^2 / 4}{1 + |
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\theta^2 / 4} |
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\end{array} |
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\right). |
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\end{equation} |
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All other rotations follow in a straightforward manner. |
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After the first part of the propagation, the forces and body-fixed |
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torques are calculated at the new positions and orientations |
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{\tt doForces:} |
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\begin{align*} |
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{\bf f}(t + h) &\leftarrow |
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- \left(\frac{\partial V}{\partial {\bf r}}\right)_{{\bf r}(t + h)}, \\ |
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% |
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{\bf \tau}^{s}(t + h) &\leftarrow {\bf u}(t + h) |
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\times \frac{\partial V}{\partial {\bf u}}, \\ |
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% |
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{\bf \tau}^{b}(t + h) &\leftarrow \mathsf{A}(t + h) |
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\cdot {\bf \tau}^s(t + h). |
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\end{align*} |
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{\sc oopse} automatically updates ${\bf u}$ when the rotation matrix |
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$\mathsf{A}$ is calculated in {\tt moveA}. Once the forces and |
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torques have been obtained at the new time step, the velocities can |
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be advanced to the same time value. |
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{\tt moveB:} |
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\begin{align*} |
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{\bf v}\left(t + h \right) &\leftarrow {\bf v}\left(t + h / 2 |
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\right) |
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+ \frac{h}{2} \left( {\bf f}(t + h) / m \right), \\ |
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% |
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{\bf j}\left(t + h \right) &\leftarrow {\bf j}\left(t + h / 2 |
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\right) |
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+ \frac{h}{2} {\bf \tau}^b(t + h) . |
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\end{align*} |
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The matrix rotations used in the DLM method end up being more costly |
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computationally than the simpler arithmetic quaternion propagation. |
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With the same time step, a 1000-molecule water simulation shows an |
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average 7\% increase in computation time using the DLM method in |
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place of quaternions. This cost is more than justified when |
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comparing the energy conservation of the two methods as illustrated |
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in Fig.~\ref{timestep}. |
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\begin{figure} |
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\centering |
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\includegraphics[width=\linewidth]{timeStep.eps} |
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\caption[Energy conservation for quaternion versus DLM |
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dynamics]{Energy conservation using quaternion based integration |
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versus the method proposed by Dullweber \emph{et al.} with |
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increasing time step. For each time step, the dotted line is total |
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energy using the DLM integrator, and the solid line comes from the |
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quaternion integrator. The larger time step plots are shifted up |
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from the true energy baseline for clarity.} \label{timestep} |
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\end{figure} |
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In Fig.~\ref{timestep}, the resulting energy drift at various time |
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steps for both the DLM and quaternion integration schemes is |
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compared. All of the 1000 molecule water simulations started with |
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the same configuration, and the only difference was the method for |
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handling rotational motion. At time steps of 0.1 and 0.5 fs, both |
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methods for propagating molecule rotation conserve energy fairly |
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well, with the quaternion method showing a slight energy drift over |
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time in the 0.5 fs time step simulation. At time steps of 1 and 2 |
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fs, the energy conservation benefits of the DLM method are clearly |
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demonstrated. Thus, while maintaining the same degree of energy |
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conservation, one can take considerably longer time steps, leading |
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to an overall reduction in computation time. |
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\subsection{\label{methodSection:NVT}Nos\'{e}-Hoover Thermostatting} |
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The Nos\'e-Hoover equations of motion are given by\cite{Hoover85} |
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\begin{eqnarray} |
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\dot{{\bf r}} & = & {\bf v}, \\ |
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\dot{{\bf v}} & = & \frac{{\bf f}}{m} - \chi {\bf v} ,\\ |
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\dot{\mathsf{A}} & = & \mathsf{A} \cdot |
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\mbox{ skew}\left(\overleftrightarrow{\mathsf{I}}^{-1} \cdot {\bf j}\right), \\ |
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\dot{{\bf j}} & = & {\bf j} \times \left( |
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\overleftrightarrow{\mathsf{I}}^{-1} \cdot {\bf j} \right) - \mbox{ |
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rot}\left(\mathsf{A}^{T} \cdot \frac{\partial V}{\partial |
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\mathsf{A}} \right) - \chi {\bf j}. \label{eq:nosehoovereom} |
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\end{eqnarray} |
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$\chi$ is an ``extra'' variable included in the extended system, and |
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it is propagated using the first order equation of motion |
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\begin{equation} |
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\dot{\chi} = \frac{1}{\tau_{T}^2} \left( |
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\frac{T}{T_{\mathrm{target}}} - 1 \right). \label{eq:nosehooverext} |
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\end{equation} |
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The instantaneous temperature $T$ is proportional to the total |
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kinetic energy (both translational and orientational) and is given |
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by |
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\begin{equation} |
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T = \frac{2 K}{f k_B} |
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\end{equation} |
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Here, $f$ is the total number of degrees of freedom in the system, |
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\begin{equation} |
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f = 3 N + 3 N_{\mathrm{orient}} - N_{\mathrm{constraints}}, |
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\end{equation} |
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and $K$ is the total kinetic energy, |
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\begin{equation} |
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K = \sum_{i=1}^{N} \frac{1}{2} m_i {\bf v}_i^T \cdot {\bf v}_i + |
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\sum_{i=1}^{N_{\mathrm{orient}}} \frac{1}{2} {\bf j}_i^T \cdot |
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\overleftrightarrow{\mathsf{I}}_i^{-1} \cdot {\bf j}_i. |
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\end{equation} |
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In eq.(\ref{eq:nosehooverext}), $\tau_T$ is the time constant for |
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relaxation of the temperature to the target value. To set values |
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for $\tau_T$ or $T_{\mathrm{target}}$ in a simulation, one would use |
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the {\tt tauThermostat} and {\tt targetTemperature} keywords in the |
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{\tt .bass} file. The units for {\tt tauThermostat} are fs, and the |
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units for the {\tt targetTemperature} are degrees K. The |
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integration of the equations of motion is carried out in a |
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velocity-Verlet style 2 part algorithm: |
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{\tt moveA:} |
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\begin{align*} |
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T(t) &\leftarrow \left\{{\bf v}(t)\right\}, \left\{{\bf j}(t)\right\} ,\\ |
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% |
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{\bf v}\left(t + h / 2\right) &\leftarrow {\bf v}(t) |
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+ \frac{h}{2} \left( \frac{{\bf f}(t)}{m} - {\bf v}(t) |
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\chi(t)\right), \\ |
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% |
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{\bf r}(t + h) &\leftarrow {\bf r}(t) |
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+ h {\bf v}\left(t + h / 2 \right) ,\\ |
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% |
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{\bf j}\left(t + h / 2 \right) &\leftarrow {\bf j}(t) |
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+ \frac{h}{2} \left( {\bf \tau}^b(t) - {\bf j}(t) |
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\chi(t) \right) ,\\ |
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% |
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\mathsf{A}(t + h) &\leftarrow \mathrm{rotate} |
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\left(h * {\bf j}(t + h / 2) |
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\overleftrightarrow{\mathsf{I}}^{-1} \right) ,\\ |
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% |
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\chi\left(t + h / 2 \right) &\leftarrow \chi(t) |
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+ \frac{h}{2 \tau_T^2} \left( \frac{T(t)} |
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{T_{\mathrm{target}}} - 1 \right) . |
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\end{align*} |
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Here $\mathrm{rotate}(h * {\bf j} |
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\overleftrightarrow{\mathsf{I}}^{-1})$ is the same symplectic |
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Trotter factorization of the three rotation operations that was |
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discussed in the section on the DLM integrator. Note that this |
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operation modifies both the rotation matrix $\mathsf{A}$ and the |
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angular momentum ${\bf j}$. {\tt moveA} propagates velocities by a |
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half time step, and positional degrees of freedom by a full time |
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step. The new positions (and orientations) are then used to |
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calculate a new set of forces and torques in exactly the same way |
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they are calculated in the {\tt doForces} portion of the DLM |
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integrator. |
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Once the forces and torques have been obtained at the new time step, |
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the temperature, velocities, and the extended system variable can be |
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advanced to the same time value. |
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{\tt moveB:} |
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\begin{align*} |
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T(t + h) &\leftarrow \left\{{\bf v}(t + h)\right\}, |
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\left\{{\bf j}(t + h)\right\}, \\ |
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% |
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\chi\left(t + h \right) &\leftarrow \chi\left(t + h / |
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2 \right) + \frac{h}{2 \tau_T^2} \left( \frac{T(t+h)} |
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{T_{\mathrm{target}}} - 1 \right), \\ |
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% |
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{\bf v}\left(t + h \right) &\leftarrow {\bf v}\left(t |
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+ h / 2 \right) + \frac{h}{2} \left( |
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\frac{{\bf f}(t + h)}{m} - {\bf v}(t + h) |
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\chi(t h)\right) ,\\ |
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% |
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{\bf j}\left(t + h \right) &\leftarrow {\bf j}\left(t |
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+ h / 2 \right) + \frac{h}{2} |
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\left( {\bf \tau}^b(t + h) - {\bf j}(t + h) |
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\chi(t + h) \right) . |
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\end{align*} |
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Since ${\bf v}(t + h)$ and ${\bf j}(t + h)$ are required to |
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caclculate $T(t + h)$ as well as $\chi(t + h)$, they indirectly |
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depend on their own values at time $t + h$. {\tt moveB} is |
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therefore done in an iterative fashion until $\chi(t + h)$ becomes |
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self-consistent. The relative tolerance for the self-consistency |
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check defaults to a value of $\mbox{10}^{-6}$, but {\sc oopse} will |
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terminate the iteration after 4 loops even if the consistency check |
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has not been satisfied. |
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The Nos\'e-Hoover algorithm is known to conserve a Hamiltonian for |
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the extended system that is, to within a constant, identical to the |
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Helmholtz free energy,\cite{melchionna93} |
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\begin{equation} |
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H_{\mathrm{NVT}} = V + K + f k_B T_{\mathrm{target}} \left( |
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\frac{\tau_{T}^2 \chi^2(t)}{2} + \int_{0}^{t} \chi(t^\prime) |
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dt^\prime \right). |
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\end{equation} |
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Poor choices of $h$ or $\tau_T$ can result in non-conservation of |
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$H_{\mathrm{NVT}}$, so the conserved quantity is maintained in the |
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last column of the {\tt .stat} file to allow checks on the quality |
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of the integration. |
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Bond constraints are applied at the end of both the {\tt moveA} and |
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{\tt moveB} portions of the algorithm. Details on the constraint |
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algorithms are given in section \ref{oopseSec:rattle}. |
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\subsection{\label{methodSection:NPTi}Constant-pressure integration with |
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isotropic box deformations (NPTi)} |
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To carry out isobaric-isothermal ensemble calculations {\sc oopse} |
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implements the Melchionna modifications to the |
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Nos\'e-Hoover-Andersen equations of motion,\cite{melchionna93} |
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\begin{eqnarray} |
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\dot{{\bf r}} & = & {\bf v} + \eta \left( {\bf r} - {\bf R}_0 \right), \\ |
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\dot{{\bf v}} & = & \frac{{\bf f}}{m} - (\eta + \chi) {\bf v}, \\ |
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\dot{\mathsf{A}} & = & \mathsf{A} \cdot |
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\mbox{ skew}\left(\overleftrightarrow{I}^{-1} \cdot {\bf j}\right),\\ |
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\dot{{\bf j}} & = & {\bf j} \times \left( |
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\overleftrightarrow{I}^{-1} \cdot {\bf j} \right) - \mbox{ |
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rot}\left(\mathsf{A}^{T} \cdot \frac{\partial |
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V}{\partial \mathsf{A}} \right) - \chi {\bf j}, \\ |
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\dot{\chi} & = & \frac{1}{\tau_{T}^2} \left( |
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\frac{T}{T_{\mathrm{target}}} - 1 \right) ,\\ |
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\dot{\eta} & = & \frac{1}{\tau_{B}^2 f k_B T_{\mathrm{target}}} V |
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\left( P - |
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P_{\mathrm{target}} \right), \\ |
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\dot{\mathcal{V}} & = & 3 \mathcal{V} \eta . \label{eq:melchionna1} |
324 |
|
|
\end{eqnarray} |
325 |
|
|
|
326 |
|
|
$\chi$ and $\eta$ are the ``extra'' degrees of freedom in the |
327 |
|
|
extended system. $\chi$ is a thermostat, and it has the same |
328 |
|
|
function as it does in the Nos\'e-Hoover NVT integrator. $\eta$ is |
329 |
|
|
a barostat which controls changes to the volume of the simulation |
330 |
|
|
box. ${\bf R}_0$ is the location of the center of mass for the |
331 |
|
|
entire system, and $\mathcal{V}$ is the volume of the simulation |
332 |
|
|
box. At any time, the volume can be calculated from the determinant |
333 |
|
|
of the matrix which describes the box shape: |
334 |
|
|
\begin{equation} |
335 |
|
|
\mathcal{V} = \det(\mathsf{H}). |
336 |
|
|
\end{equation} |
337 |
|
|
|
338 |
|
|
The NPTi integrator requires an instantaneous pressure. This |
339 |
|
|
quantity is calculated via the pressure tensor, |
340 |
|
|
\begin{equation} |
341 |
|
|
\overleftrightarrow{\mathsf{P}}(t) = \frac{1}{\mathcal{V}(t)} \left( |
342 |
|
|
\sum_{i=1}^{N} m_i {\bf v}_i(t) \otimes {\bf v}_i(t) \right) + |
343 |
|
|
\overleftrightarrow{\mathsf{W}}(t). |
344 |
|
|
\end{equation} |
345 |
|
|
The kinetic contribution to the pressure tensor utilizes the {\it |
346 |
|
|
outer} product of the velocities denoted by the $\otimes$ symbol. |
347 |
|
|
The stress tensor is calculated from another outer product of the |
348 |
|
|
inter-atomic separation vectors (${\bf r}_{ij} = {\bf r}_j - {\bf |
349 |
|
|
r}_i$) with the forces between the same two atoms, |
350 |
|
|
\begin{equation} |
351 |
|
|
\overleftrightarrow{\mathsf{W}}(t) = \sum_{i} \sum_{j>i} {\bf |
352 |
|
|
r}_{ij}(t) \otimes {\bf f}_{ij}(t). |
353 |
|
|
\end{equation} |
354 |
|
|
The instantaneous pressure is then simply obtained from the trace of |
355 |
|
|
the Pressure tensor, |
356 |
|
|
\begin{equation} |
357 |
|
|
P(t) = \frac{1}{3} \mathrm{Tr} \left( |
358 |
|
|
\overleftrightarrow{\mathsf{P}}(t). \right) |
359 |
|
|
\end{equation} |
360 |
|
|
|
361 |
|
|
In eq.(\ref{eq:melchionna1}), $\tau_B$ is the time constant for |
362 |
|
|
relaxation of the pressure to the target value. To set values for |
363 |
|
|
$\tau_B$ or $P_{\mathrm{target}}$ in a simulation, one would use the |
364 |
|
|
{\tt tauBarostat} and {\tt targetPressure} keywords in the {\tt |
365 |
|
|
.bass} file. The units for {\tt tauBarostat} are fs, and the units |
366 |
|
|
for the {\tt targetPressure} are atmospheres. Like in the NVT |
367 |
|
|
integrator, the integration of the equations of motion is carried |
368 |
|
|
out in a velocity-Verlet style 2 part algorithm: |
369 |
|
|
|
370 |
|
|
{\tt moveA:} |
371 |
|
|
\begin{align*} |
372 |
|
|
T(t) &\leftarrow \left\{{\bf v}(t)\right\}, \left\{{\bf j}(t)\right\} ,\\ |
373 |
|
|
% |
374 |
|
|
P(t) &\leftarrow \left\{{\bf r}(t)\right\}, \left\{{\bf v}(t)\right\} ,\\ |
375 |
|
|
% |
376 |
|
|
{\bf v}\left(t + h / 2\right) &\leftarrow {\bf v}(t) |
377 |
|
|
+ \frac{h}{2} \left( \frac{{\bf f}(t)}{m} - {\bf v}(t) |
378 |
|
|
\left(\chi(t) + \eta(t) \right) \right), \\ |
379 |
|
|
% |
380 |
|
|
{\bf j}\left(t + h / 2 \right) &\leftarrow {\bf j}(t) |
381 |
|
|
+ \frac{h}{2} \left( {\bf \tau}^b(t) - {\bf j}(t) |
382 |
|
|
\chi(t) \right), \\ |
383 |
|
|
% |
384 |
|
|
\mathsf{A}(t + h) &\leftarrow \mathrm{rotate}\left(h * |
385 |
|
|
{\bf j}(t + h / 2) \overleftrightarrow{\mathsf{I}}^{-1} |
386 |
|
|
\right) ,\\ |
387 |
|
|
% |
388 |
|
|
\chi\left(t + h / 2 \right) &\leftarrow \chi(t) + |
389 |
|
|
\frac{h}{2 \tau_T^2} \left( \frac{T(t)}{T_{\mathrm{target}}} - 1 |
390 |
|
|
\right) ,\\ |
391 |
|
|
% |
392 |
|
|
\eta(t + h / 2) &\leftarrow \eta(t) + \frac{h |
393 |
|
|
\mathcal{V}(t)}{2 N k_B T(t) \tau_B^2} \left( P(t) |
394 |
|
|
- P_{\mathrm{target}} \right), \\ |
395 |
|
|
% |
396 |
|
|
{\bf r}(t + h) &\leftarrow {\bf r}(t) + h |
397 |
|
|
\left\{ {\bf v}\left(t + h / 2 \right) |
398 |
|
|
+ \eta(t + h / 2)\left[ {\bf r}(t + h) |
399 |
|
|
- {\bf R}_0 \right] \right\} ,\\ |
400 |
|
|
% |
401 |
|
|
\mathsf{H}(t + h) &\leftarrow e^{-h \eta(t + h / 2)} |
402 |
|
|
\mathsf{H}(t). |
403 |
|
|
\end{align*} |
404 |
|
|
|
405 |
|
|
Most of these equations are identical to their counterparts in the |
406 |
|
|
NVT integrator, but the propagation of positions to time $t + h$ |
407 |
|
|
depends on the positions at the same time. {\sc oopse} carries out |
408 |
|
|
this step iteratively (with a limit of 5 passes through the |
409 |
|
|
iterative loop). Also, the simulation box $\mathsf{H}$ is scaled |
410 |
|
|
uniformly for one full time step by an exponential factor that |
411 |
|
|
depends on the value of $\eta$ at time $t + h / 2$. Reshaping the |
412 |
|
|
box uniformly also scales the volume of the box by |
413 |
|
|
\begin{equation} |
414 |
|
|
\mathcal{V}(t + h) \leftarrow e^{ - 3 h \eta(t + h /2)}. |
415 |
|
|
\mathcal{V}(t) |
416 |
|
|
\end{equation} |
417 |
|
|
|
418 |
|
|
The {\tt doForces} step for the NPTi integrator is exactly the same |
419 |
|
|
as in both the DLM and NVT integrators. Once the forces and torques |
420 |
|
|
have been obtained at the new time step, the velocities can be |
421 |
|
|
advanced to the same time value. |
422 |
|
|
|
423 |
|
|
{\tt moveB:} |
424 |
|
|
\begin{align*} |
425 |
|
|
T(t + h) &\leftarrow \left\{{\bf v}(t + h)\right\}, |
426 |
|
|
\left\{{\bf j}(t + h)\right\} ,\\ |
427 |
|
|
% |
428 |
|
|
P(t + h) &\leftarrow \left\{{\bf r}(t + h)\right\}, |
429 |
|
|
\left\{{\bf v}(t + h)\right\}, \\ |
430 |
|
|
% |
431 |
|
|
\chi\left(t + h \right) &\leftarrow \chi\left(t + h / |
432 |
|
|
2 \right) + \frac{h}{2 \tau_T^2} \left( \frac{T(t+h)} |
433 |
|
|
{T_{\mathrm{target}}} - 1 \right), \\ |
434 |
|
|
% |
435 |
|
|
\eta(t + h) &\leftarrow \eta(t + h / 2) + |
436 |
|
|
\frac{h \mathcal{V}(t + h)}{2 N k_B T(t + h) |
437 |
|
|
\tau_B^2} \left( P(t + h) - P_{\mathrm{target}} \right), \\ |
438 |
|
|
% |
439 |
|
|
{\bf v}\left(t + h \right) &\leftarrow {\bf v}\left(t |
440 |
|
|
+ h / 2 \right) + \frac{h}{2} \left( |
441 |
|
|
\frac{{\bf f}(t + h)}{m} - {\bf v}(t + h) |
442 |
|
|
(\chi(t + h) + \eta(t + h)) \right) ,\\ |
443 |
|
|
% |
444 |
|
|
{\bf j}\left(t + h \right) &\leftarrow {\bf j}\left(t |
445 |
|
|
+ h / 2 \right) + \frac{h}{2} \left( {\bf |
446 |
|
|
\tau}^b(t + h) - {\bf j}(t + h) |
447 |
|
|
\chi(t + h) \right) . |
448 |
|
|
\end{align*} |
449 |
|
|
|
450 |
|
|
Once again, since ${\bf v}(t + h)$ and ${\bf j}(t + h)$ are required |
451 |
|
|
to caclculate $T(t + h)$, $P(t + h)$, $\chi(t + h)$, and $\eta(t + |
452 |
|
|
h)$, they indirectly depend on their own values at time $t + h$. |
453 |
|
|
{\tt moveB} is therefore done in an iterative fashion until $\chi(t |
454 |
|
|
+ h)$ and $\eta(t + h)$ become self-consistent. The relative |
455 |
|
|
tolerance for the self-consistency check defaults to a value of |
456 |
|
|
$\mbox{10}^{-6}$, but {\sc oopse} will terminate the iteration after |
457 |
|
|
4 loops even if the consistency check has not been satisfied. |
458 |
|
|
|
459 |
|
|
The Melchionna modification of the Nos\'e-Hoover-Andersen algorithm |
460 |
|
|
is known to conserve a Hamiltonian for the extended system that is, |
461 |
|
|
to within a constant, identical to the Gibbs free energy, |
462 |
|
|
\begin{equation} |
463 |
|
|
H_{\mathrm{NPTi}} = V + K + f k_B T_{\mathrm{target}} \left( |
464 |
|
|
\frac{\tau_{T}^2 \chi^2(t)}{2} + \int_{0}^{t} \chi(t^\prime) |
465 |
|
|
dt^\prime \right) + P_{\mathrm{target}} \mathcal{V}(t). |
466 |
|
|
\end{equation} |
467 |
|
|
Poor choices of $\delta t$, $\tau_T$, or $\tau_B$ can result in |
468 |
|
|
non-conservation of $H_{\mathrm{NPTi}}$, so the conserved quantity |
469 |
|
|
is maintained in the last column of the {\tt .stat} file to allow |
470 |
|
|
checks on the quality of the integration. It is also known that |
471 |
|
|
this algorithm samples the equilibrium distribution for the enthalpy |
472 |
|
|
(including contributions for the thermostat and barostat), |
473 |
|
|
\begin{equation} |
474 |
|
|
H_{\mathrm{NPTi}} = V + K + \frac{f k_B T_{\mathrm{target}}}{2} |
475 |
|
|
\left( \chi^2 \tau_T^2 + \eta^2 \tau_B^2 \right) + |
476 |
|
|
P_{\mathrm{target}} \mathcal{V}(t). |
477 |
|
|
\end{equation} |
478 |
|
|
|
479 |
|
|
Bond constraints are applied at the end of both the {\tt moveA} and |
480 |
|
|
{\tt moveB} portions of the algorithm. Details on the constraint |
481 |
|
|
algorithms are given in section \ref{oopseSec:rattle}. |
482 |
|
|
|
483 |
|
|
\subsection{\label{methodSection:NPTf}Constant-pressure integration with a |
484 |
|
|
flexible box (NPTf)} |
485 |
|
|
|
486 |
|
|
There is a relatively simple generalization of the |
487 |
|
|
Nos\'e-Hoover-Andersen method to include changes in the simulation |
488 |
|
|
box {\it shape} as well as in the volume of the box. This method |
489 |
|
|
utilizes the full $3 \times 3$ pressure tensor and introduces a |
490 |
|
|
tensor of extended variables ($\overleftrightarrow{\eta}$) to |
491 |
|
|
control changes to the box shape. The equations of motion for this |
492 |
|
|
method are |
493 |
|
|
\begin{eqnarray} |
494 |
|
|
\dot{{\bf r}} & = & {\bf v} + \overleftrightarrow{\eta} \cdot \left( {\bf r} - {\bf R}_0 \right), \\ |
495 |
|
|
\dot{{\bf v}} & = & \frac{{\bf f}}{m} - (\overleftrightarrow{\eta} + |
496 |
|
|
\chi \cdot \mathsf{1}) {\bf v}, \\ |
497 |
|
|
\dot{\mathsf{A}} & = & \mathsf{A} \cdot |
498 |
|
|
\mbox{ skew}\left(\overleftrightarrow{I}^{-1} \cdot {\bf j}\right) ,\\ |
499 |
|
|
\dot{{\bf j}} & = & {\bf j} \times \left( |
500 |
|
|
\overleftrightarrow{I}^{-1} \cdot {\bf j} \right) - \mbox{ |
501 |
|
|
rot}\left(\mathsf{A}^{T} \cdot \frac{\partial |
502 |
|
|
V}{\partial \mathsf{A}} \right) - \chi {\bf j} ,\\ |
503 |
|
|
\dot{\chi} & = & \frac{1}{\tau_{T}^2} \left( |
504 |
|
|
\frac{T}{T_{\mathrm{target}}} - 1 \right) ,\\ |
505 |
|
|
\dot{\overleftrightarrow{\eta}} & = & \frac{1}{\tau_{B}^2 f k_B |
506 |
|
|
T_{\mathrm{target}}} V \left( \overleftrightarrow{\mathsf{P}} - P_{\mathrm{target}}\mathsf{1} \right) ,\\ |
507 |
|
|
\dot{\mathsf{H}} & = & \overleftrightarrow{\eta} \cdot \mathsf{H} . |
508 |
|
|
\label{eq:melchionna2} |
509 |
|
|
\end{eqnarray} |
510 |
|
|
|
511 |
|
|
Here, $\mathsf{1}$ is the unit matrix and |
512 |
|
|
$\overleftrightarrow{\mathsf{P}}$ is the pressure tensor. Again, |
513 |
|
|
the volume, $\mathcal{V} = \det \mathsf{H}$. |
514 |
|
|
|
515 |
|
|
The propagation of the equations of motion is nearly identical to |
516 |
|
|
the NPTi integration: |
517 |
|
|
|
518 |
|
|
{\tt moveA:} |
519 |
|
|
\begin{align*} |
520 |
|
|
T(t) &\leftarrow \left\{{\bf v}(t)\right\}, \left\{{\bf j}(t)\right\} ,\\ |
521 |
|
|
% |
522 |
|
|
\overleftrightarrow{\mathsf{P}}(t) &\leftarrow \left\{{\bf |
523 |
|
|
r}(t)\right\}, |
524 |
|
|
\left\{{\bf v}(t)\right\} ,\\ |
525 |
|
|
% |
526 |
|
|
{\bf v}\left(t + h / 2\right) &\leftarrow {\bf v}(t) |
527 |
|
|
+ \frac{h}{2} \left( \frac{{\bf f}(t)}{m} - |
528 |
|
|
\left(\chi(t)\mathsf{1} + \overleftrightarrow{\eta}(t) \right) \cdot |
529 |
|
|
{\bf v}(t) \right), \\ |
530 |
|
|
% |
531 |
|
|
{\bf j}\left(t + h / 2 \right) &\leftarrow {\bf j}(t) |
532 |
|
|
+ \frac{h}{2} \left( {\bf \tau}^b(t) - {\bf j}(t) |
533 |
|
|
\chi(t) \right), \\ |
534 |
|
|
% |
535 |
|
|
\mathsf{A}(t + h) &\leftarrow \mathrm{rotate}\left(h * |
536 |
|
|
{\bf j}(t + h / 2) \overleftrightarrow{\mathsf{I}}^{-1} |
537 |
|
|
\right), \\ |
538 |
|
|
% |
539 |
|
|
\chi\left(t + h / 2 \right) &\leftarrow \chi(t) + |
540 |
|
|
\frac{h}{2 \tau_T^2} \left( \frac{T(t)}{T_{\mathrm{target}}} |
541 |
|
|
- 1 \right), \\ |
542 |
|
|
% |
543 |
|
|
\overleftrightarrow{\eta}(t + h / 2) &\leftarrow |
544 |
|
|
\overleftrightarrow{\eta}(t) + \frac{h \mathcal{V}(t)}{2 N k_B |
545 |
|
|
T(t) \tau_B^2} \left( \overleftrightarrow{\mathsf{P}}(t) |
546 |
|
|
- P_{\mathrm{target}}\mathsf{1} \right), \\ |
547 |
|
|
% |
548 |
|
|
{\bf r}(t + h) &\leftarrow {\bf r}(t) + h \left\{ {\bf v} |
549 |
|
|
\left(t + h / 2 \right) + \overleftrightarrow{\eta}(t + |
550 |
|
|
h / 2) \cdot \left[ {\bf r}(t + h) |
551 |
|
|
- {\bf R}_0 \right] \right\}, \\ |
552 |
|
|
% |
553 |
|
|
\mathsf{H}(t + h) &\leftarrow \mathsf{H}(t) \cdot e^{-h |
554 |
|
|
\overleftrightarrow{\eta}(t + h / 2)} . |
555 |
|
|
\end{align*} |
556 |
|
|
{\sc oopse} uses a power series expansion truncated at second order |
557 |
|
|
for the exponential operation which scales the simulation box. |
558 |
|
|
|
559 |
|
|
The {\tt moveB} portion of the algorithm is largely unchanged from |
560 |
|
|
the NPTi integrator: |
561 |
|
|
|
562 |
|
|
{\tt moveB:} |
563 |
|
|
\begin{align*} |
564 |
|
|
T(t + h) &\leftarrow \left\{{\bf v}(t + h)\right\}, |
565 |
|
|
\left\{{\bf j}(t + h)\right\}, \\ |
566 |
|
|
% |
567 |
|
|
\overleftrightarrow{\mathsf{P}}(t + h) &\leftarrow \left\{{\bf r} |
568 |
|
|
(t + h)\right\}, \left\{{\bf v}(t |
569 |
|
|
+ h)\right\}, \left\{{\bf f}(t + h)\right\} ,\\ |
570 |
|
|
% |
571 |
|
|
\chi\left(t + h \right) &\leftarrow \chi\left(t + h / |
572 |
|
|
2 \right) + \frac{h}{2 \tau_T^2} \left( \frac{T(t+ |
573 |
|
|
h)}{T_{\mathrm{target}}} - 1 \right), \\ |
574 |
|
|
% |
575 |
|
|
\overleftrightarrow{\eta}(t + h) &\leftarrow |
576 |
|
|
\overleftrightarrow{\eta}(t + h / 2) + |
577 |
|
|
\frac{h \mathcal{V}(t + h)}{2 N k_B T(t + h) |
578 |
|
|
\tau_B^2} \left( \overleftrightarrow{P}(t + h) |
579 |
|
|
- P_{\mathrm{target}}\mathsf{1} \right) ,\\ |
580 |
|
|
% |
581 |
|
|
{\bf v}\left(t + h \right) &\leftarrow {\bf v}\left(t |
582 |
|
|
+ h / 2 \right) + \frac{h}{2} \left( |
583 |
|
|
\frac{{\bf f}(t + h)}{m} - |
584 |
|
|
(\chi(t + h)\mathsf{1} + \overleftrightarrow{\eta}(t |
585 |
|
|
+ h)) \right) \cdot {\bf v}(t + h), \\ |
586 |
|
|
% |
587 |
|
|
{\bf j}\left(t + h \right) &\leftarrow {\bf j}\left(t |
588 |
|
|
+ h / 2 \right) + \frac{h}{2} \left( {\bf \tau}^b(t |
589 |
|
|
+ h) - {\bf j}(t + h) \chi(t + h) \right) . |
590 |
|
|
\end{align*} |
591 |
|
|
|
592 |
|
|
The iterative schemes for both {\tt moveA} and {\tt moveB} are |
593 |
|
|
identical to those described for the NPTi integrator. |
594 |
|
|
|
595 |
|
|
The NPTf integrator is known to conserve the following Hamiltonian: |
596 |
|
|
\begin{equation} |
597 |
|
|
H_{\mathrm{NPTf}} = V + K + f k_B T_{\mathrm{target}} \left( |
598 |
|
|
\frac{\tau_{T}^2 \chi^2(t)}{2} + \int_{0}^{t} \chi(t^\prime) |
599 |
|
|
dt^\prime \right) + P_{\mathrm{target}} \mathcal{V}(t) + \frac{f k_B |
600 |
|
|
T_{\mathrm{target}}}{2} |
601 |
|
|
\mathrm{Tr}\left[\overleftrightarrow{\eta}(t)\right]^2 \tau_B^2. |
602 |
|
|
\end{equation} |
603 |
|
|
|
604 |
|
|
This integrator must be used with care, particularly in liquid |
605 |
|
|
simulations. Liquids have very small restoring forces in the |
606 |
|
|
off-diagonal directions, and the simulation box can very quickly |
607 |
|
|
form elongated and sheared geometries which become smaller than the |
608 |
|
|
electrostatic or Lennard-Jones cutoff radii. The NPTf integrator |
609 |
|
|
finds most use in simulating crystals or liquid crystals which |
610 |
|
|
assume non-orthorhombic geometries. |
611 |
|
|
|
612 |
tim |
2739 |
\subsection{\label{methodSection:otherSpecialEnsembles}Other Special Ensembles} |
613 |
tim |
2729 |
|
614 |
tim |
2776 |
\subsubsection{\label{methodSection:NPAT}NPAT Ensemble} |
615 |
tim |
2729 |
|
616 |
tim |
2739 |
A comprehensive understanding of structure¨Cfunction relations of |
617 |
|
|
biological membrane system ultimately relies on structure and |
618 |
|
|
dynamics of lipid bilayer, which are strongly affected by the |
619 |
|
|
interfacial interaction between lipid molecules and surrounding |
620 |
|
|
media. One quantity to describe the interfacial interaction is so |
621 |
|
|
called the average surface area per lipid. Constat area and constant |
622 |
|
|
lateral pressure simulation can be achieved by extending the |
623 |
|
|
standard NPT ensemble with a different pressure control strategy |
624 |
tim |
2798 |
|
625 |
tim |
2729 |
\begin{equation} |
626 |
tim |
2798 |
\.{\overleftrightarrow{{\eta _{\alpha \beta}}}}=\left\{\begin{array}{ll} |
627 |
|
|
\frac{{V(P_{\alpha \beta } - P_{{\rm{target}}} )}}{{\tau_{\rm{B}}^{\rm{2}} fk_B T_{{\rm{target}}} }} |
628 |
|
|
& \mbox{if \[ \alpha = \beta = z)$}\\ |
629 |
|
|
0 & \mbox{otherwise}\\ |
630 |
|
|
\end{array} |
631 |
|
|
\right. |
632 |
tim |
2729 |
\end{equation} |
633 |
tim |
2798 |
|
634 |
tim |
2739 |
Note that the iterative schemes for NPAT are identical to those |
635 |
|
|
described for the NPTi integrator. |
636 |
tim |
2729 |
|
637 |
tim |
2776 |
\subsubsection{\label{methodSection:NPrT}NP$\gamma$T Ensemble} |
638 |
tim |
2729 |
|
639 |
tim |
2739 |
Theoretically, the surface tension $\gamma$ of a stress free |
640 |
|
|
membrane system should be zero since its surface free energy $G$ is |
641 |
|
|
minimum with respect to surface area $A$ |
642 |
|
|
\[ |
643 |
|
|
\gamma = \frac{{\partial G}}{{\partial A}}. |
644 |
|
|
\] |
645 |
|
|
However, a surface tension of zero is not appropriate for relatively |
646 |
|
|
small patches of membrane. In order to eliminate the edge effect of |
647 |
tim |
2776 |
the membrane simulation, a special ensemble, NP$\gamma$T, is |
648 |
|
|
proposed to maintain the lateral surface tension and normal |
649 |
|
|
pressure. The equation of motion for cell size control tensor, |
650 |
tim |
2778 |
$\eta$, in $NP\gamma T$ is |
651 |
tim |
2729 |
\begin{equation} |
652 |
tim |
2798 |
\.{\overleftrightarrow{{\eta _{\alpha \beta}}}}=\left\{\begin{array}{ll} |
653 |
|
|
- A_{xy} (\gamma _\alpha - \gamma _{{\rm{target}}} ) & \mbox{$\alpha = \beta = x$ or $\alpha = \beta = y$}\\ |
654 |
|
|
\frac{{V(P_{\alpha \beta } - P_{{\rm{target}}} )}}{{\tau _{\rm{B}}^{\rm{2}} fk_B T_{{\rm{target}}}}} & \mbox{$\alpha = \beta = z$} \\ |
655 |
|
|
0 & \mbox{$\alpha \ne \beta$} \\ |
656 |
|
|
\right. |
657 |
tim |
2729 |
\end{equation} |
658 |
tim |
2739 |
where $ \gamma _{{\rm{target}}}$ is the external surface tension and |
659 |
|
|
the instantaneous surface tensor $\gamma _\alpha$ is given by |
660 |
tim |
2729 |
\begin{equation} |
661 |
tim |
2739 |
\gamma _\alpha = - h_z |
662 |
|
|
(\mathord{\buildrel{\lower3pt\hbox{$\scriptscriptstyle\leftrightarrow$}} |
663 |
|
|
\over P} _{\alpha \alpha } - P_{{\rm{target}}} ) |
664 |
|
|
\label{methodEquation:instantaneousSurfaceTensor} |
665 |
tim |
2729 |
\end{equation} |
666 |
|
|
|
667 |
tim |
2739 |
There is one additional extended system integrator (NPTxyz), in |
668 |
|
|
which each attempt to preserve the target pressure along the box |
669 |
|
|
walls perpendicular to that particular axis. The lengths of the box |
670 |
|
|
axes are allowed to fluctuate independently, but the angle between |
671 |
|
|
the box axes does not change. It should be noted that the NPTxyz |
672 |
|
|
integrator is a special case of $NP\gamma T$ if the surface tension |
673 |
|
|
$\gamma$ is set to zero. |
674 |
tim |
2729 |
|
675 |
tim |
2776 |
%\section{\label{methodSection:constraintMethod}Constraint Method} |
676 |
|
|
|
677 |
|
|
%\subsection{\label{methodSection:bondConstraint}Bond Constraint for Rigid Body} |
678 |
|
|
|
679 |
|
|
%\subsection{\label{methodSection:zcons}Z-constraint Method} |
680 |
|
|
|
681 |
tim |
2685 |
\section{\label{methodSection:langevin}Integrators for Langevin Dynamics of Rigid Bodies} |
682 |
|
|
|
683 |
tim |
2729 |
\subsection{\label{methodSection:temperature}Temperature Control} |
684 |
tim |
2685 |
|
685 |
tim |
2729 |
\subsection{\label{methodSection:pressureControl}Pressure Control} |
686 |
|
|
|
687 |
|
|
\section{\label{methodSection:hydrodynamics}Hydrodynamics} |
688 |
|
|
|
689 |
|
|
%\section{\label{methodSection:coarseGrained}Coarse-Grained Modeling} |
690 |
|
|
|
691 |
|
|
%\section{\label{methodSection:moleculeScale}Molecular-Scale Modeling} |