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Constant pressure molecular dynamics algorithms
, 1994Modularly invariant equations of motion are derived that generate the isothermal–isobaric ensemble as their phase space averages. Isotropic volume fluctuations and fully flexible simulation cells as well as a hybrid scheme that naturally combines the two
G. Martyna, D. Tobias, M. Klein
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Molecular dynamics and lattice dynamics calculations in molecular crystals
Physica B+C, 1985Abstract Molecular dynamics and lattice dynamics represent two complementary approaches to the study of the static and dynamical properties of molecular crystals. The different fields of application for the two techniques are illustrated and the complementary informations obtainable are discussed. Special attention is payed to the study of anharmonic
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Molecular Dynamics with Molecular Temperature
The Journal of Physical Chemistry A, 2004The difficulty in simulating a large number of large molecules lies in the enormous difference in time scale between translational and intramolecular motions. If a molecular dynamics simulation is to model an event of microsecond duration, a computation time step on the order of a femtosecond is still required, making the simulation virtually ...
Denis J. Phares, Arun R. Srinivasa
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Molecular modelling and molecular dynamics of CFTR
Cellular and Molecular Life Sciences, 2016The cystic fibrosis transmembrane conductance regulator (CFTR) protein is a member of the ATP-binding cassette (ABC) transporter superfamily that functions as an ATP-gated channel. Considerable progress has been made over the last years in the understanding of the molecular basis of the CFTR functions, as well as dysfunctions causing the common genetic
Brice Hoffmann +3 more
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1990
The basic methodology of equilibrium molecular dynamics is described. Examples from the literature are used to illustrate how molecular dynamics has been used to resolve theoretical controversies, provide data to test theories, and occasionally to discover new phenomena.
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The basic methodology of equilibrium molecular dynamics is described. Examples from the literature are used to illustrate how molecular dynamics has been used to resolve theoretical controversies, provide data to test theories, and occasionally to discover new phenomena.
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Molecular Dynamics of Gangliosides
2018Computational methodologies have immense potential to delineate the dynamic conformations of glycoconjugates including gangliosides, thereby characterizing the conformational adaptability of their glycans upon interacting with various target proteins.
Koichi Kato +3 more
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Molecular Spectra and Molecular Dynamics [PDF]
Nature, 1952 Molecular Spectra and Molecular Structure 1: Spectra of Diatomic Molecules. By Gerhard Herzberg. Second edition. Pp. xv + 658. (New York: D. Van Nostrand Co., Inc.; London: Macmillan and Co., Ltd., 1950.) 9.75 dollars; 73s. 6d. net.
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Molecular dynamics simulations of structure and dynamics of organic molecular crystals
Physical Chemistry Chemical Physics, 2010A set of model compounds covering a range of polarity and flexibility have been simulated using GAFF, CHARMM22, OPLS and MM3 force fields to examine how well classical molecular dynamics simulations can reproduce structural and dynamic aspects of organic molecular crystals.
Alexandra Nemkevich +4 more
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VMD: visual molecular dynamics.
Journal of Molecular Graphics, 1996W. Humphrey, A. Dalke, K. Schulten
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Ab initio molecular dynamics for liquid metals.
Physical Review B (Condensed Matter), 1995G. Kresse, J. Hafner
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