Molecular dynamics simulation applications

Hermans, J. Pathiaseril, A. Anderson, A., Excess free-energy of liquids from molecular-dynamics simulations — application to water models, J. Am. Chem. Soc. 1988,110, 5982-5986. 

We also note that ah initio techniques implemented in a standard fashion, that is, without simulated annealing for iterative determination of the electronic wave function, have been combined with geometry optimization or molecular dynamics simulation. Applications include molecular dynamics of dense helium [7] and Si , n = 4,6,8,10 [8] using gradients calculated at the HF level, and simulated annealing geometry optimization of LisH at the HF and MP2 level [9]... 

W. Swaminathan, W. E. Harte, and D. L. Beveridge, /. Am. Chem. Soc., 113, 2717 (1991). Investigation of Domain Structure in Proteins via Molecular Dynamics Simulation Application to HlV-1 Protease Dimer. 

Carre, A., Horbach, J., Ispas, S., and Kob, W. (2008) New fitting scheme to obtain effective potential from Car-Parrinello molecular-dynamics simulations application to sihca, Eur. Lett., 82,17001. 

Takenaka N, Kitamura Y, Koyano Y, Nagaoka M (2012) The number-adaptive multiscale QM/MM molecular dynamics simulation application to liquid water. Chem Phys Lett 524 56-61... 

Bartell and co-workers have made significant progress by combining electron diffraction studies from beams of molecular clusters with molecular dynamics simulations [14, 51, 52]. Due to their small volumes, deep supercoolings can be attained in cluster beams however, the temperature is not easily controlled. The rapid nucleation that ensues can produce new phases not observed in the bulk [14]. Despite the concern about the appropriateness of the classic model for small clusters, its application appears to be valid in several cases [51]. 

Bala, R, Lesyng, B., McCammon, J.A. Extended Hellmann-Feynman theorem for non-stationary states and its application in quantum-classical molecular dynamics simulations. Chem. Phys. Lett. 219 (1994) 259-266. 

Schlitter et al., 1993] Schlitter, J., Engels, M., Kruger, P., Jacoby, E., and Wollmer, A. Targeted molecular dynamics simulation of conformational change - application to the t <- r transition in insulin. Molecular Simulation. 10 (1993) 291-308... 

J. D. Turner, P. K. Weiner, H. M. Chun, V. Lupi, S. Gallion, and U. C. Singh. Variable reduction techniques applied to molecular dynamics simulations. In W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson, editors. Computer Simulation of Biomolecular Systems Theoretical and Experimental Applications, volume 2, chapter 24. ESCOM, Leiden, The Netherlands, 1993. 

Applications of Ab-Initio Molecular Dynamics Simulations in Chemistry and Polymer Science... 

Although, the notion of molecular dynamics was known in the early turn of the century, the first conscious effort in the use of computer for molecular dynamics simulation was made by Alder and Wainright, who in their paper [1] reported the application of molecular dynamics to realistic particle systems. Using hard spheres potential and fastest computers at the time, they were able to simulate systems of 32 to 108 atoms in 10 to 30 hours. Since the work of Alder and Wainright, interests in MD have increased tremendously, see... 

The visualization of volumetric properties is more important in other scientific disciplines (e.g., computer tomography in medicine, or convection streams in geology). However, there are also some applications in chemistry (Figure 2-125d), among which only the distribution of water density in molecular dynamics simulations will be mentioned here. Computer visualization of this property is usually realized with two or three dimensional textures [203]. 

Gunsteren W F and H J C Berendsen 1990. Computer Simulation of Molecular Dynamics Methodology, Applications and Perspectives in Chemistry. Angewandte Chemie International Edition in English 29 992-1023. 

Choose an initial set of atom positions. The same techniques used for molecular dynamics simulations are applicable. 

See van Gunsteren, W.F. Berendsen, H.J.C. Computer simulation of molecular dynamics-methodology, applications, and perspectives in chemistry Angewandre Chemie, International Edition in English, 29 992-1023, 1990, and Karplus, M. Petsko, G.A. Molecular dynamics simulations in biology Nature 347 631-639, 1990. 

T Ichiye, RB Yelle, JB Koerner, PD Swartz, BW Beck. Molecular dynamics simulation studies of electron transfer properties of Ee-S proteins. Biomacromolecules Erom 3-D Structure to Applications. Hanford Symposium on Health and the Environment 34, Pasco, WA, 1995, pp 203-213. 

K. Binder. General aspects of computer simulation techniques and their applications in polymer physics. In K. Binder, ed. Monte Carlo and Molecular Dynamics Simulations in Polymer Science. New York Oxford University Press, 1995, pp. 3 1. 

Molecular Workbench (MW) is a two-dimensional molecular dynamics application written in Java and created by Concord Consortium (http //workbench.concord.org/). It provides multiple representations and molecular dynamic simulations that allow... 

It is worth noting that much of the development work for the MM force fields has centred on low energy structures of molecules. Consequently, some of the force constants are less applicable to higher energy molecular structures that can occur in molecular dynamics simulations of liquid crystals. 

The field of electrochemical ion transfer reactions (EITRs) is relatively recent compared with that of electron transfer reactions, and the application of molecular dynamics simulations to study this phenomenon dates from the 1990s. The simulations may shed light on various aspects of the EITR. One of the key questions on this problem is if EITR can be interpreted in the same grounds as those employed to understand electron transfer reactions (ETRs). Eor example, let us consider the electrochemical oxidation reaction of iodine ... 

Equation (4-5) can be directly utilized in statistical mechanical Monte Carlo and molecular dynamics simulations by choosing an appropriate QM model, balancing computational efficiency and accuracy, and MM force fields for biomacromolecules and the solvent water. Our group has extensively explored various QM/MM methods using different quantum models, ranging from semiempirical methods to ab initio molecular orbital and valence bond theories to density functional theory, applied to a wide range of applications in chemistry and biology. Some of these studies have been discussed before and they are not emphasized in this article. We focus on developments that have not been often discussed. 

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