Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userSelf-Healing Umbrella Sampling: Convergence and efficiency
327
0
0.0
(
0
)
Authors
G. Fort
Ask ChatGPT about the research
No Arabic abstract
The Self-Healing Umbrella Sampling (SHUS) algorithm is an adaptive biasing algorithm which has been proposed to efficiently sample a multimodal probability measure. We show that this method can be seen as a variant of the well-known Wang-Landau algorithm. Adapting results on the convergence of the Wang-Landau algorithm, we prove the convergence of the SHUS algorithm. We also compare the two methods in terms of efficiency. We finally propose a modification of the SHUS algorithm in order to increase its efficiency, and exhibit some similarities of SHUS with the well-tempered metadynamics method.
rate research
Read More
We consider a generalization of the discrete-time Self Healing Umbrella Sampling method, which is an adaptive importance technique useful to sample multimodal target distributions. The importance function is based on the weights (namely the relative probabilities) of disjoint sets which form a partition of the space. These weights are unknown but are learnt on the fly yielding an adaptive algorithm. In the context of computational statistical physics, the logarithm of these weights is, up to a multiplicative constant, the free energy, and the discrete valued function defining the partition is called the collective variable. The algorithm falls into the general class of Wang-Landau type methods, and is a generalization of the original Self Healing Umbrella Sampling method in two ways: (i) the updating strategy leads to a larger penalization strength of already visited sets in order to escape more quickly from metastable states, and (ii) the target distribution is biased using only a fraction of the free energy, in order to increase the effective sample size and reduce the variance of importance sampling estimators. The algorithm can also be seen as a generalization of well-tempered metadynamics. We prove the convergence of the algorithm and analyze numerically its efficiency on a toy example.
Water density fluctuations are an important statistical mechanical observable that is related to many-body correlations, as well as hydrophobic hydration and interactions. Local water density fluctuations at a solid-water surface have also been proposed as a measure of its hydrophobicity. These fluctuations can be quantified by calculating the probability, $P_v(N)$, of observing $N$ waters in a probe volume of interest $v$. When $v$ is large, calculating $P_v(N)$ using molecular dynamics simulations is challenging, as the probability of observing very few waters is exponentially small, and the standard procedure for overcoming this problem (umbrella sampling in $N$) leads to undesirable impulsive forces. Patel et al. [J. Phys. Chem. B, 114, 1632 (2010)] have recently developed an indirect umbrella sampling (INDUS) method, that samples a coarse-grained particle number to obtain $P_v(N)$ in cuboidal volumes. Here, we present and demonstrate an extension of that approach to other basic shapes, like spheres and cylinders, as well as to collections of such volumes. We further describe the implementation of INDUS in the NPT ensemble and calculate $P_v(N)$ distributions over a broad range of pressures. Our method may be of particular interest in characterizing the hydrophobicity of interfaces of proteins, nanotubes and related systems.
We describe and analyze some Monte Carlo methods for manifolds in Euclidean space defined by equality and inequality constraints. First, we give an MCMC sampler for probability distributions defined by un-normalized densities on such manifolds. The sampler uses a specific orthogonal projection to the surface that requires only information about the tangent space to the manifold, obtainable from first derivatives of the constraint functions, hence avoiding the need for curvature information or second derivatives. Second, we use the sampler to develop a multi-stage algorithm to compute integrals over such manifolds. We provide single-run error estimates that avoid the need for multiple independent runs. Computational experiments on various test problems show that the algorithms and error estimates work in practice. The method is applied to compute the entropies of different sticky hard sphere systems. These predict the temperature or interaction energy at which loops of hard sticky spheres become preferable to chains.
Anomalous transport in a circular comb is considered. The circular motion takes place for a fixed radius, while radii are continuously distributed along the circle. Two scenarios of the anomalous transport, related to the reflecting and periodic angular boundary conditions, are studied. The first scenario with the reflection boundary conditions for the circular diffusion corresponds to the conformal mapping of a 2D comb Fokker-Planck equation on the circular comb. This topologically constraint motion is named umbrella comb model. In this case, the reflecting boundary conditions are imposed on the circular (rotator) motion, while the radial motion corresponds to geometric Brownian motion with vanishing to zero boundary conditions on infinity. The radial diffusion is described by the log-normal distribution, which corresponds to exponentially fast motion with the mean squared displacement (MSD) of the order of $e^t$. The second scenario corresponds to the circular diffusion with periodic boundary conditions and the outward radial diffusion with vanishing to zero boundary conditions at infinity. In this case the radial motion corresponds to normal diffusion. The circular motion in both scenarios is a superposition of cosine functions that results in the stationary Bernoulli polynomials for the probability distributions.
The equations of the temperature-accelerated molecular dynamics (TAMD) method for the calculations of free energies and partition functions are analyzed. Specifically, the exponential convergence of the law of these stochastic processes is established, with a convergence rate close to the one of the limiting, effective dynamics at higher temperature obtained with infinite acceleration. It is also shown that the invariant measures of TAMD are close to a known reference measure, with an error that can be quantified precisely. Finally, a Central Limit Theorem is proven, which allows the estimation of errors on properties calculated by ergodic time averages. These results not only demonstrate the usefulness and validity range of the TAMD equations, but they also permit in principle to adjust the parameter in these equations to optimize their efficiency.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
