Download PDF by Mikael P. Johansson, Ville R. I. Kaila, Dage Sundholm: Biomolecular Simulations: Methods and Protocols

By Mikael P. Johansson, Ville R. I. Kaila, Dage Sundholm (auth.), Luca Monticelli, Emppu Salonen (eds.)

ISBN-10: 1627030166

ISBN-13: 9781627030168

ISBN-10: 1627030174

ISBN-13: 9781627030175

Over the previous forty years the sector of molecular simulations has developed from picosecond stories of remoted macromolecules in vacuum to reviews of complicated, chemically heterogeneous organic structures inclusive of hundreds of thousands of atoms, with the simulation time scales spanning as much as milliseconds. In Biomolecular Simulations: tools and Protocols, specialist researchers illustrate some of the tools regular in molecular modelling of organic structures, together with tools for digital constitution calculations, classical molecular dynamics simulations and coarse-grained thoughts. a range of complicated options and up to date methodological advancements, which hardly locate assurance in conventional textbooks, can be brought.

Written within the hugely profitable Methods in Molecular Biology sequence structure, chapters comprise common introductions to well-established computational methodologies, functions to real-world organic platforms, in addition to useful tips and common protocols on engaging in biomolecular simulations. designated emphasis is put on simulations of proteins, lipids, nucleic acids, and carbohydrates. Authoritative and functional, Biomolecular Simulations: tools and Protocols seeks to assist scientists in extra simulation reports of organic platforms.

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Extra info for Biomolecular Simulations: Methods and Protocols

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J Chem Phys 114:9758–9763 8. Todorova T, Seitsonen AP, Hutter J, Kuo I-FW, Mundy CJ (2006) Molecular dynamics simulation of liquid water: hybrid density functionals.

Hohenberg P, Kohn W (1964) Inhomogeneous electron gas. Phys Rev 136: B864–B871 61. Kohn W, Sham LJ (1965) Self-consistent equations including exchange and correlation effects. Phys Rev 140:A1133–A1138 62. Thomas LH (1927) The calculation of atomic fields. Proc Cambridge Phil Soc 23:542–548 63. Fermi E (1927) Un metodo statistico per la determinazione di alcune prioprieta dell’atomo. Rend Accad Naz Lincei 6:602–607 64. Ceperly DM, Alder BJ (1980) Ground state of the electron gas by a stochastic method.

With the latest algorithms, this is the case. The BOMD trajectories are sensitive to the wave function convergence criterion, and good convergence is needed to achieve the same stability as in CPMD. Convergence (the largest element of the wave function gradient) of the order of 10À6 is needed. A good presentation of the stability of BOMD can be found in Hutter’s lectures in Ref. (4). 4. Quantum Chemistry Besides dynamics, it is essential to choose the quantum chemical method to treat the electrons.

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Biomolecular Simulations: Methods and Protocols by Mikael P. Johansson, Ville R. I. Kaila, Dage Sundholm (auth.), Luca Monticelli, Emppu Salonen (eds.)

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