An Infinite Swapping Approach to the Rare-Event Sampling Problem

We describe a new approach to the rare-event Monte Carlo sampling problem. This technique utilizes a symmetrization strategy to create probability distributions that are more highly connected and thus more easily sampled than their original, potentially sparse counterparts. After discussing the formal outline of the approach and devising techniques for its practical implementation, we illustrate the utility of the technique with a series of numerical applications to Lennard-Jones clusters of varying complexity and rare-event character.Comment: 24 pages, 16 figure

A Multiscale Approach to Determination of Thermal Properties and Changes in Free Energy: Application to Reconstruction of Dislocations in Silicon

We introduce an approach to exploit the existence of multiple levels of description of a physical system to radically accelerate the determination of thermodynamic quantities. We first give a proof of principle of the method using two empirical interatomic potential functions. We then apply the technique to feed information from an interatomic potential into otherwise inaccessible quantum mechanical tight-binding calculations of the reconstruction of partial dislocations in silicon at finite temperature. With this approach, comprehensive ab initio studies at finite temperature will now be possible.Comment: 5 pages, 3 figure

Nondielectric long-range solvation of polar liquids in cubic symmetry

Long-range solvation properties of strongly coupled dipolar systems simulated using the Ewald and reaction field methods are assessed by using electric fluctuation formulas for a dielectric medium. Some components of the fluctuating electric multipole moments are suppressed, whereas other components are favored as the boundary of the simulation box is approached. An analysis of electrostatic interactions in a periodic cubic system suggests that these structural effects are due to the periodicity embedded in the Ewald method. Furthermore, the results obtained using the reaction field method are very similar to those obtained using the Ewald method, an effect which we attribute to the use of toroidal boundary conditions in the former case. Thus, the long-range solvation properties of polar liquids simulated using either of the two methods are nondielectric in their character. (C) 2009 American Institute of Physics. [doi:10.1063/1.3250941

Multicanonical Multigrid Monte Carlo

To further improve the performance of Monte Carlo simulations of first-order phase transitions we propose to combine the multicanonical approach with multigrid techniques. We report tests of this proposition for the $d$-dimensional $\Phi^4$ field theory in two different situations. First, we study quantum tunneling for $d = 1$ in the continuum limit, and second, we investigate first-order phase transitions for $d = 2$ in the infinite volume limit. Compared with standard multicanonical simulations we obtain improvement factors of several resp. of about one order of magnitude.Comment: 12 pages LaTex, 1 PS figure appended. FU-Berlin preprint FUB-HEP 9/9

Temperature and density extrapolations in canonical ensemble Monte Carlo simulations

We show how to use the multiple histogram method to combine canonical ensemble Monte Carlo simulations made at different temperatures and densities. The method can be applied to study systems of particles with arbitrary interaction potential and to compute the thermodynamic properties over a range of temperatures and densities. The calculation of the Helmholtz free energy relative to some thermodynamic reference state enables us to study phase coexistence properties. We test the method on the Lennard-Jones fluids for which many results are available.Comment: 5 pages, 3 figure

A Hydrophobic Gate in an Ion Channel: The Closed State of the Nicotinic Acetylcholine Receptor

The nicotinic acetylcholine receptor (nAChR) is the prototypic member of the `Cys-loop' superfamily of ligand-gated ion channels which mediate synaptic neurotransmission, and whose other members include receptors for glycine, gamma-aminobutyric acid, and serotonin. Cryo-electron microscopy has yielded a three dimensional structure of the nAChR in its closed state. However, the exact nature and location of the channel gate remains uncertain. Although the transmembrane pore is constricted close to its center, it is not completely occluded. Rather, the pore has a central hydrophobic zone of radius about 3 A. Model calculations suggest that such a constriction may form a hydrophobic gate, preventing movement of ions through a channel. We present a detailed and quantitative simulation study of the hydrophobic gating model of the nicotinic receptor, in order to fully evaluate this hypothesis. We demonstrate that the hydrophobic constriction of the nAChR pore indeed forms a closed gate. Potential of mean force (PMF) calculations reveal that the constriction presents a barrier of height ca. 10 kT to the permeation of sodium ions, placing an upper bound on the closed channel conductance of 0.3 pS. Thus, a 3 A radius hydrophobic pore can form a functional barrier to the permeation of a 1 A radius Na+ ion. Using a united atom force field for the protein instead of an all atom one retains the qualitative features but results in differing conductances, showing that the PMF is sensitive to the detailed molecular interactions.Comment: Accepted by Physical Biology; includes a supplement and a supplementary mpeg movie can be found at http://sbcb.bioch.ox.ac.uk/oliver/download/Movies/watergate.mp

Monte Carlo simulation of a two-dimensional continuum Coulomb gas

We study the classical two-dimensional Coulomb gas model for thermal vortex fluctuations in thin superconducting/superfluid films by Monte Carlo simulation of a grand canonical vortex ensemble defined on a continuum. The Kosterlitz-Thouless transition is well understood at low vortex density, but at high vortex density the nature of the phase diagram and of the vortex phase transition is less clear. From our Monte Carlo data we construct phase diagrams for the 2D Coulomb gas without any restrictions on the vortex density. For negative vortex chemical potential (positive vortex core energy) we always find a Kosterlitz-Thouless transition. Only if the Coulomb interaction is supplemented with a short-distance repulsion, a first order transition line is found, above some positive value of the vortex chemical potential.Comment: 10 pages RevTeX, 7 postscript figures included using eps

Parallel Excluded Volume Tempering for Polymer Melts

We have developed a technique to accelerate the acquisition of effectively uncorrelated configurations for off-lattice models of dense polymer melts which makes use of both parallel tempering and large scale Monte Carlo moves. The method is based upon simulating a set of systems in parallel, each of which has a slightly different repulsive core potential, such that a thermodynamic path from full excluded volume to an ideal gas of random walks is generated. While each system is run with standard stochastic dynamics, resulting in an NVT ensemble, we implement the parallel tempering through stochastic swaps between the configurations of adjacent potentials, and the large scale Monte Carlo moves through attempted pivot and translation moves which reach a realistic acceptance probability as the limit of the ideal gas of random walks is approached. Compared to pure stochastic dynamics, this results in an increased efficiency even for a system of chains as short as $N = 60$ monomers, however at this chain length the large scale Monte Carlo moves were ineffective. For even longer chains the speedup becomes substantial, as observed from preliminary data for $N = 200$

CHARMM: The biomolecular simulation program

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983. © 2009 Wiley Periodicals, Inc.J Comput Chem, 2009.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/63074/1/21287_ftp.pd