Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
TL;DR: In this paper, the authors describe the use of arbitrary sampling distributions chosen to facilitate the estimate of the free energy difference between a model system and some reference system, but the conventional Monte Carlo methods of obtaining such averages are inadequate for the free-energy case.
About: This article is published in Journal of Computational Physics.The article was published on 1977-02-01. It has received 5058 citations till now. The article focuses on the topics: Importance sampling & Slice sampling.
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TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.
Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.
14,558 citations
Cites methods from "Nonphysical sampling distributions ..."
...The popular umbrella sampling method [71,72], whereby the probability to find the system along a given reaction coordinate is sought, falls evidently into the first category....
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...As a computational technique, SMD bears similarities to the method of umbrella sampling [71,72], which also seeks to improve the sampling of a particular degree of freedom in a biomolecular system; however, while umbrella sampling requires a series of equilibrium simulations, SMD simulations apply a constant or time-varying force which results in significant deviations from equilibrium....
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TL;DR: An improved and extended version of the coarse grained lipid model is presented, coined the MARTINI force field, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds to reproduce the free energies of these chemical building blocks.
Abstract: We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To reproduce the free energies of these chemical building blocks, the number of possible interaction levels of the coarse-grained sites has increased compared to those of the previous model. Application of the new model to lipid bilayers shows an improved behavior in terms of the stress profile across the bilayer and the tendency to form pores. An extension of the force field now also allows the simulation of planar (ring) compounds, including sterols. Application to a bilayer/cholesterol system at various concentrations shows the typical cholesterol condensation effect similar to that observed in all atom representations.
4,580 citations
TL;DR: This work presents PLUMED 2 here—a complete rewrite of the code in an object-oriented programming language (C++), which introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs.
2,256 citations
TL;DR: A method for determining the free-energy dependence on a selected number of collective variables using an adaptive bias and the formalism provides a unified description which has metadynamics and canonical sampling as limiting cases.
Abstract: We present a method for determining the free-energy dependence on a selected number of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting cases. Convergence and errors can be rigorously and easily controlled. The parameters of the simulation can be tuned so as to focus the computational effort only on the physically relevant regions of the order parameter space. The algorithm is tested on the reconstruction of an alanine dipeptide free-energy landscape.
2,174 citations
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TL;DR: In this article, a modified Monte Carlo integration over configuration space is used to investigate the properties of a two-dimensional rigid-sphere system with a set of interacting individual molecules, and the results are compared to free volume equations of state and a four-term virial coefficient expansion.
Abstract: A general method, suitable for fast computing machines, for investigating such properties as equations of state for substances consisting of interacting individual molecules is described. The method consists of a modified Monte Carlo integration over configuration space. Results for the two‐dimensional rigid‐sphere system have been obtained on the Los Alamos MANIAC and are presented here. These results are compared to the free volume equation of state and to a four‐term virial coefficient expansion.
35,161 citations
TL;DR: In this article, the equilibrium properties of a system of 864 particles interacting through a Lennard-Jones potential have been integrated for various values of the temperature and density, relative, generally, to a fluid state.
Abstract: The equation of motion of a system of 864 particles interacting through a Lennard-Jones potential has been integrated for various values of the temperature and density, relative, generally, to a fluid state. The equilibrium properties have been calculated and are shown to agree very well with the corresponding properties of argon. It is concluded that, to a good approximation, the equilibrium state of argon can be described through a two-body potential.
7,564 citations
TL;DR: In this paper, the free energy of a Lennard-Jones fluid in the liquid-vapour coexistence region was estimated by relating it to that of the inverse-twelve (soft sphere) fluid, which itself shows no condensation.
1,179 citations
TL;DR: In this paper, Monte Carlo computations have been performed in order to determine the phase transitions of a system of particles interacting through a Lennard-Jones potential, and an indirect determination of the phase transition of the hard-sphere gas is made which is essentially in agreement with the results of more direct calculations.
Abstract: Monte Carlo computations have been performed in order to determine the phase transitions of a system of particles interacting through a Lennard-Jones potential. The fluid-solid transition has been investigated using a method recently introduced by Hoover and Ree. For the liquid-gas transition a method has been devised which forces the system to remain always homogeneous. A comparison is made with experiment in the case of argon. An indirect determination of the phase transition of the hard-sphere gas is made which is essentially in agreement with the results of the more direct calculations.
1,101 citations
TL;DR: In this paper, the pressure and entropy for soft-sphere particles interacting with an inverse twelfth-power potential were determined using the Monte Carlo method, and the results were compared with the predictions of the virial series, lattice dynamics, perturbation theories, and cell models.
Abstract: The pressure and entropy for soft‐sphere particles interacting with an inverse twelfth‐power potential are determined using the Monte Carlo method. The solid‐phase entropy is calculated in two ways: by integrating the single‐occupancy equation of state from the low density limit to solid densities, and by using solid‐phase Monte Carlo pressures to evaluate the anharmonic corrections to the lattice‐dynamics high‐density limit. The two methods agree, and the entropy is used to locate the melting transition. The computed results are compared with the predictions of the virial series, lattice dynamics, perturbation theories, and cell models. For the fluid phase, perturbation theory is very accurate up to two‐thirds of the freezing density. For the solid phase, a correlated cell model predicts pressures very close to the Monte Carlo results.
287 citations