Literature DB >> 16238371

Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method: "Umbrella integration".

Johannes Kästner1, Walter Thiel.   

Abstract

We present a method to analyze biased molecular-dynamics and Monte Carlo simulations, also known as umbrella sampling. In the limiting case of a strong bias, this method is equivalent to thermodynamic integration. It employs only quantities with easily controllable equilibration and greatly reduces the statistical errors compared to the standard weighted histogram analysis method. We show the success of our approach for two examples, one analytic function, and one biological system.

Year:  2005        PMID: 16238371     DOI: 10.1063/1.2052648

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  48 in total

1.  Impact of mutation on proton transfer reactions in ketosteroid isomerase: insights from molecular dynamics simulations.

Authors:  Dhruva K Chakravorty; Sharon Hammes-Schiffer
Journal:  J Am Chem Soc       Date:  2010-06-02       Impact factor: 15.419

2.  The Role of Gln61 in HRas GTP hydrolysis: a quantum mechanics/molecular mechanics study.

Authors:  Fernando Martín-García; Jesús Ignacio Mendieta-Moreno; Eduardo López-Viñas; Paulino Gómez-Puertas; Jesús Mendieta
Journal:  Biophys J       Date:  2012-01-03       Impact factor: 4.033

3.  A dynamic view of enzyme catalysis.

Authors:  Aurora Jiménez; Pere Clapés; Ramon Crehuet
Journal:  J Mol Model       Date:  2008-03-06       Impact factor: 1.810

4.  Implementation of umbrella integration within the framework of the empirical valence bond approach.

Authors:  Dhruva K Chakravorty; Malika Kumarasiri; Alexander V Soudackov; Sharon Hammes-Schiffer
Journal:  J Chem Theory Comput       Date:  2008       Impact factor: 6.006

Review 5.  Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods.

Authors:  Hao Hu; Weitao Yang
Journal:  Annu Rev Phys Chem       Date:  2008       Impact factor: 12.703

6.  Determination of free energy profiles by repository based adaptive umbrella sampling: bridging nonequilibrium and quasiequilibrium simulations.

Authors:  Han Zheng; Yingkai Zhang
Journal:  J Chem Phys       Date:  2008-05-28       Impact factor: 3.488

7.  Communication: Iteration-free, weighted histogram analysis method in terms of intensive variables.

Authors:  Jaegil Kim; Thomas Keyes; John E Straub
Journal:  J Chem Phys       Date:  2011-08-14       Impact factor: 3.488

8.  Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI.

Authors:  Victor Ovchinnikov; Martin Karplus; Eric Vanden-Eijnden
Journal:  J Chem Phys       Date:  2011-02-28       Impact factor: 3.488

9.  Computational approach for ranking mutant enzymes according to catalytic reaction rates.

Authors:  Malika Kumarasiri; Gregory A Baker; Alexander V Soudackov; Sharon Hammes-Schiffer
Journal:  J Phys Chem B       Date:  2009-03-19       Impact factor: 2.991

10.  A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations.

Authors:  Tai-Sung Lee; Brian K Radak; Anna Pabis; Darrin M York
Journal:  J Chem Theory Comput       Date:  2012-12-12       Impact factor: 6.006

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