Quantifying density fluctuations in volumes of all shapes and sizes using indirect umbrella sampling

DOI10.1007/S10955-011-0269-9zbMATH Open1231.82079arXiv1105.0895OpenAlexW3105197180WikidataQ39878068 ScholiaQ39878068MaRDI QIDQ657808FDOQ657808

Authors: Amish J. Patel, Patrick Varilly, Shekhar Garde, David B. Chandler 

Publication date: 10 January 2012

Published in: Journal of Statistical Physics (Search for Journal in Brave)

Abstract: 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.

Full work available at URL: https://arxiv.org/abs/1105.0895

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zbMATH Keywords

density fluctuationsumbrella samplinghydrophobicityfree energy calculations

Mathematics Subject Classification ID

Statistical mechanics of liquids (82D15)

Cites Work

• Fast parallel algorithms for short-range molecular dynamics
• Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations
• The Potential Distribution Theorem and Models of Molecular Solutions

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