✦ LIBER ✦

Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling

✍ Scribed by Lu, Nandou; Kofke, David A.

Book ID: 111982222
Publisher: American Institute of Physics
Year: 2001
Tongue: English
Weight: 368 KB
Volume: 114
Category: Article
ISSN: 0021-9606
DOI: 10.1063/1.1359181

No coin nor oath required. For personal study only.

📜 SIMILAR VOLUMES

Shuttling Process in [2]Rotaxanes. Model

Shuttling Process in [2]Rotaxanes. Modeling by Molecular Dynamics and Free Energy Perturbation Simulations

✍ Grabuleda, Xavi; Ivanov, Petko; Jaime, Carlos 📂 Article 📅 2003 🏛 American Chemical Society 🌐 English ⚖ 300 KB

A Multisite Ion Model that Improves Free

A Multisite Ion Model that Improves Free Energy Calculations in Molecular Dynamics Simulations

✍ Saxena, Akansha; Sept, David 📂 Article 📅 2012 🏛 Biophysical Society 🌐 English ⚖ 35 KB

Free energy perturbation and molecular d

Free energy perturbation and molecular dynamics calculations of copper binding to azurin

✍ Matteo Pappalardo; Danilo Milardi; Domenico M. Grasso; Carmelo La Rosa 📂 Article 📅 2003 🏛 John Wiley and Sons 🌐 English ⚖ 184 KB

## Abstract Free energy perturbation/molecular dynamics simulations have been carried out on copper/azurin systems calculating the binding affinities of copper (II) ion to azurin either in the native or in the unfolded state. In order to test the validity of the strategy adopted for the calculation

Multisite Ion Models That Improve Coordi

Multisite Ion Models That Improve Coordination and Free Energy Calculations in Molecular Dynamics Simulations

✍ Saxena, Akansha; Sept, David 📂 Article 📅 2013 🏛 American Chemical Society 🌐 English ⚖ 957 KB

Calculation of ligand binding free energ

Calculation of ligand binding free energies from molecular dynamics simulations

✍ J. Marelius; T. Hansson; J. Åqvist 📂 Article 📅 1998 🏛 John Wiley and Sons 🌐 English ⚖ 247 KB 👁 3 views

A recently developed method for predicting binding affinities in ligand᎐receptor complexes, based on interaction energy averaging and conformational sampling by molecular dynamics simulation, is presented. Polar and nonpolar contributions to the binding free energy are approximated by a linear scali

Some practical aspects of free energy ca

Some practical aspects of free energy calculations from molecular dynamics simulation

✍ Sen, Srikanta; Nilsson, Lennart 📂 Article 📅 1999 🏛 John Wiley and Sons 🌐 English ⚖ 211 KB 👁 3 views

In this work, we address two critical aspects of calculation of the free energy differences in molecular systems from molecular simulations. The first aspect involves checking whether the calculated free energy difference depends significantly on the extent of perturbation used for accomplishment of