ArticleThe Journal of chemical physics2006
Free volume hypothetical scanning molecular dynamics method for the absolute free energy of liquids.
Article in The Journal of chemical physics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Relative stability of the open and closed conformations of the active site loop of streptavidin.The Journal of chemical physics · 2011Article
- Entropy and Free Energy of a Mobile Loop Based on the Crystal Structures of the Free and Bound Proteins.Entropy (Basel, Switzerland) · 2010Article
- Absolute free energy and entropy of a mobile loop of the enzyme acetylcholinesterase.The journal of physical chemistry. B · 2009Article
- Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding.Current protein & peptide science · 2009Review
- Entropy and free energy of a mobile protein loop in explicit water.The journal of physical chemistry. B · 2008Article
- Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics.Journal of molecular recognition : JMRArticle
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Authors and funding
2 authors.
Funding
Abstract
The hypothetical scanning (HS) method is a general approach for calculating the absolute entropy, S, and free energy, F, by analyzing Boltzmann samples obtained by Monte Carlo (MC) or molecular dynamics (MD) techniques. With HS applied to a fluid, each configuration i of the sample is reconstructed by gradually placing the molecules in their positions at i using transition probabilities (TPs). With our recent version of HS, called HSMC-EV, each TP is calculated from MC simulations, where the simulated particles are excluded from the volume reconstructed in previous steps. In this paper we remove the excluded volume (EV) restriction, replacing it by a "free volume" (FV) approach. For liquid argon, HSMC-FV leads to an improvement in efficiency over HSMC-EV by a factor of 2-3. Importantly, the FV treatment greatly simplifies the HS implementation for liquids, allowing a much more natural application of the method for MD simulations. Given the success and popularity of MD, the present development of the HSMD method for liquids is an important advancement for HS methodology. Results for the HSMD-FV approach presented here agree well with our HSMC and thermodynamic integration results. The efficiency of HSMD-FV is equivalent to HSMC-EV. The potential use of HSMC(MD)-FV in protein systems with explicit water is discussed.
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