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Partial differential equations and stochastic methods in moleculardynamics*

Published online by Cambridge University Press:  23 May 2016

Tony Lelièvre
Affiliation:
Université Paris-Est, CERMICS (ENPC), INRIA, F-77455 Marne-la-Vallée, France E-mail: tony.lelievre@enpc.fr, gabriel.stoltz@enpc.fr
Gabriel Stoltz
Affiliation:
Université Paris-Est, CERMICS (ENPC), INRIA, F-77455 Marne-la-Vallée, France E-mail: tony.lelievre@enpc.fr, gabriel.stoltz@enpc.fr
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Abstract

The objective of molecular dynamics computations is to infer macroscopic properties of matter from atomistic models via averages with respect to probability measures dictated by the principles of statistical physics. Obtaining accurate results requires efficient sampling of atomistic configurations, which are typically generated using very long trajectories of stochastic differential equations in high dimensions, such as Langevin dynamics and its overdamped limit. Depending on the quantities of interest at the macroscopic level, one may also be interested in dynamical properties computed from averages over paths of these dynamics.

This review describes how techniques from the analysis of partial differential equations can be used to devise good algorithms and to quantify their efficiency and accuracy. In particular, a crucial role is played by the study of the long-time behaviour of the solution to the Fokker–Planck equation associated with the stochastic dynamics.

Information

Type
Research Article
Copyright
© Cambridge University Press, 2016 
Figure 0

Figure 1.1. (a, c) Level sets of the two-dimensional potentials. (b, d) Time evolution of the $x$-coordinate of the stochastic process solution to overdamped Langevin dynamics (1.8) in these potentials. (a, b) Energetic barrier (${\it\beta}=4$), (c, d) entropic barrier (${\it\beta}=10$).

Figure 1

Figure 1.2. Average exit times $\mathbb{E}({\it\tau})$ as a function of ${\it\beta}$, where ${\it\tau}=\inf \{t\geqslant 0\mid x_{t}\geqslant x_{\ast }\}$. (a) Energetic barrier (potential in Figure 1.1(a)) with $x_{\ast }=1.3$ and initial conditions $x_{0}=(-1,0)$. The average exit times increase exponentially with ${\it\beta}$ (note the logarithmic scale on the ordinate axis). (b) Entropic barrier (potential in Figure 1.1(c)) with $x_{\ast }=1.5$ and initial conditions $x_{0}=(-3,0)$. The average exit times increase linearly with ${\it\beta}$ for sufficiently large values of ${\it\beta}$.

Figure 2

Figure 1.3. Interdependence of the sections. Double (respectively triple) boxes are for sections devoted to the computation of thermodynamic quantities (respectively dynamical quantities). In particular, Section 3 mainly uses decay estimates from Section 2 on the semigroup of the form $\Vert \text{e}^{t{\mathcal{L}}}\Vert _{{\mathcal{B}}(E)}\leqslant C\,\text{e}^{-{\it\alpha}t}$ for some positive constants $C$ and ${\it\alpha}$, which in turn implies the well-posedness of the Poisson equation ${\mathcal{L}}u=f$ in a certain Banach space $E$ (see Proposition 2.1 and Corollaries 2.4, 2.16, 2.21 and 2.27).

Figure 3

Figure 4.1. To be compared with Figure 1.1. (a, b) Energetic barrier case, (c, d) entropic barrier case. (a) Level sets of the free energy biased potential. (b) Time evolution of the $x$-coordinate on the biased potential (${\it\beta}=4$). (c) Free energy. (d) Time evolution of the $x$-coordinate on the biased potential (${\it\beta}=10$).

Figure 4

Figure 4.2. (a) Trajectory of the ABF process on the model problem for an energetic barrier (see Figure 1.1), with ${\it\beta}=80$. The evolution of ${\it\xi}(X_{t})$ (i.e. the abscissa of $X_{t}$) is represented as a function of time. (b) Close-up of the first 2500 time units.

Figure 5

Figure 4.3. Average exit time from the left well as a function of the inverse temperature ${\it\beta}$, for the ABF process (squares) compared to the unbiased overdamped Langevin dynamics (circles: see also Figure 1.2(a)).

Figure 6

Figure 5.1. (a) Error in the mobility as a function of the time step ${\rm\Delta}t$ when the integrated velocity autocorrelation function is computed using a Riemann sum or with the corrected formula (5.24) in the case ${\it\alpha}=2$. The result from computing the integral using the trapezoidal rule is also shown. (b) Error in the computed average of total energy, with the correction term computed using the same step size by a discretization of (3.32) with the discrete Green–Kubo formula (5.24). Averages obtained with a reference correction computed more accurately at a smaller time step in a separate simulation are labelled as the ‘exact correction’. In both cases, ‘order ${\it\alpha}$’ means that the error scales as $C{\rm\Delta}t^{{\it\alpha}}$.

Figure 7

Figure 5.2. Linear response of the numerical approximation of the average velocity $\mathbb{E}_{{\it\eta}}(F^{T}M^{-1}p)$ as a function of ${\it\eta}$ for the scheme associated with $P_{{\rm\Delta}t}^{{\it\gamma}C,B+{\it\eta}\widetilde{{\mathcal{L}}},A,B+{\it\eta}\widetilde{{\mathcal{L}}},{\it\gamma}C}$, for ${\rm\Delta}t=0.01$. A linear fit on the first ten values gives a slope of ${\it\rho}_{F,{\rm\Delta}t}\simeq 0.07416$.

Figure 8

Figure 5.3. Estimated mobility ${\it\rho}_{F,{\rm\Delta}t}$ for the first-order scheme $P_{{\rm\Delta}t}^{A,B+{\it\eta}\widetilde{{\mathcal{L}}},{\it\gamma}C}$ and second-order scheme $P_{{\rm\Delta}t}^{{\it\gamma}C,B+{\it\eta}\widetilde{{\mathcal{L}}},A,B+{\it\eta}\widetilde{{\mathcal{L}}},{\it\gamma}C}$ as a function of the time step ${\rm\Delta}t$. The fits give ${\it\rho}_{F,{\rm\Delta}t}\simeq 0.0740+0.0817{\rm\Delta}t$ and ${\it\rho}_{F,{\rm\Delta}t}\simeq 0.0741+0.197{\rm\Delta}t^{2}$, respectively.

Figure 9

Figure 6.1. The state $S$ with the partition of the boundary $\partial S$ into four subsets $(\partial S_{i})_{i=1,\ldots ,4}$. The dashed line represents the trajectory of a dynamics entering $S$.

Figure 10

Figure 6.2. Parallel Replica. Many exit events are simulated in parallel, all starting from the QSD in $S$. The dashed line trajectory represents the reference walker, which stays sufficiently long within $S$ that we can assume the end point (circle) is distributed according to the QSD. The other dots (squares) represent i.i.d. initial conditions distributed according to the QSD. The solid line trajectories are simulated in parallel.

Figure 11

Figure 6.3. Hyperdynamics. The exit event is simulated on a biased potential in $S$. The honeycomb region $S^{-}$ represents the support of the biasing potential ${\it\delta}V$. The inset represents the original potential $V$ (black line) and the biased potential $V+{\it\delta}V$ along the axis represented by the dashed line.

Figure 12

Figure 6.4. Temperature Accelerated Dynamics. Exit events are simulated at a higher temperature and then extrapolated to the original smaller temperature.