𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Potential of mean force by thermodynamic integration: Molecular-dynamics simulation of decomplexation

✍ Scribed by J. Van Eerden; W.J. Briels; S. Harkema; D. Feil

Publisher
Elsevier Science
Year
1989
Tongue
English
Weight
566 KB
Volume
164
Category
Article
ISSN
0009-2614

No coin nor oath required. For personal study only.

✦ Synopsis

Umbrella samplmg" has been incorporated in the thermodynamic integration method to obtain a potential of mean force by slow growth molecular-dynamics simulations. The method was tested for liquid argon, for which good agreement was obtained with a standard potential of mean force, as derived from the radial pair-correlation function. For a sodium chloride ion-pair in aqueous solution the calculations showed resonable agreement with a literature result. The method was also applied to the decomplexation of 18-crown-6 and a potassium cation in aqueous solution.

📜 SIMILAR VOLUMES

Reconstructing Potentials of Mean Force
Reconstructing Potentials of Mean Force through Time Series Analysis of Steered Molecular Dynamics Simulations
✍ Justin R Gullingsrud; Rosemary Braun; Klaus Schulten 📂 Article 📅 1999 🏛 Elsevier Science 🌐 English ⚖ 158 KB

Atomic force microscopy (AFM) experiments and steered molecular dynamics (SMD) simulations have revealed much about the dynamics of protein-ligand binding and unbinding, as well as the stretching and unfolding of proteins. Both techniques induce ligand unbinding or protein unfolding by applying exte

Interfacial Excess Free Energies of Soli
Interfacial Excess Free Energies of Solid–Liquid Interfaces by Molecular Dynamics Simulation and Thermodynamic Integration
✍ Frédéric Leroy; Daniel J. V. A. dos Santos; Florian Müller-Plathe 📂 Article 📅 2009 🏛 John Wiley and Sons 🌐 English ⚖ 244 KB

## Abstract A method to compute the interfacial excess free energy of systems where a liquid phase is interacting with a solid phase is presented. The calculations are carried out by means of molecular dynamics simulations. The algorithm is based on a thermodynamic integration scheme that reversibl

Statistical thermodynamics of internal r
Statistical thermodynamics of internal rotation in a hindering potential of mean force obtained from computer simulations
✍ Vladimir Hnizdo; Adam Fedorowicz; Harshinder Singh; Eugene Demchuk 📂 Article 📅 2003 🏛 John Wiley and Sons 🌐 English ⚖ 175 KB

## Abstract A method of statistical estimation is applied to the problem of one‐dimensional internal rotation in a hindering potential of mean force. The hindering potential, which may have a completely general shape, is expanded in a Fourier series, the coefficients of which are estimated by fitti

Investigating Alanine–Silica Interaction
Investigating Alanine–Silica Interaction by Means of First-Principles Molecular-Dynamics Simulations
✍ Marco Nonella; Stefan Seeger 📂 Article 📅 2008 🏛 John Wiley and Sons 🌐 English ⚖ 673 KB

## Abstract In our attempts to achieve a detailed understanding of protein–silica interactions at an atomic level we have, as a first step, simulated a small system consisting of one alanine in different protonation states, and a hydroxylated silica surface, using a first‐principles molecular‐dynam

Evaluation of Interaction Forces between
Evaluation of Interaction Forces between Macroparticles in Simple Fluids by Molecular Dynamics Simulation
✍ Hiroyuki Shinto; Minoru Miyahara; Ko Higashitani 📂 Article 📅 1999 🏛 Elsevier Science 🌐 English ⚖ 86 KB

The present article provides the description of the solvation forces between large spheres in a fluid. The molecular dynamics (MD) method was applied to the relatively simple systems in which a pair of structureless macroparticles, either solvophobic or solvophilic, is immersed in a simple fluid of