Simulations, macromolecular systems

Plimpton, S., Hendrickson, B. A New Parallel Method for Molecular Dynamics Simulation of Macromolecular Systems. 1994. Technical Report SAND94-1862. Sandia National Laboratories. 

The highest probability paths will make the argument of the exponential small. That will be true for paths that follow Newtonian dynamics where mr = F(r). Olender and Elber [45] demonstrated how large values of the time step ht can be used in a way that projects out high frequency motions of the system and allows for the simulation of long-time molecular dynamics trajectories for macromolecular systems. 

The simulation of macromolecular systems involves, in principle, the same difficulties as that of compounds of low-molecular mass, but the polymeric nature of the molecules tends to aggravate the computational problems faced by investigators of small molecules. 

Boyd, Wiley-VCH, New York, 1998, pp. 1-74. Calculation of the Free Energy and the Entropy of Macromolecular Systems by Computer Simulation. 

It has been suggested that aqueous micellar systems simulate the electrostatic and hydrophobic interactions of the heme cavity [15-23]. Pioneering studies by Simplicio et al. [15-17] have shown that the heme is monodispersed when encapsulated in aqueous micelles. They have studied binding of cyanide and other axial ligands to ferric hemes in micellar environments. These studies [15-23] indicated that a heme encapsulated in an aqueous detergent micelle finds itself inside a large macromolecular cavity whose interactions is primarily... 

Eds., Wiley-VCH, New York, 1998, Vol. 12, pp. 1-74. Calculation of the Free Energy and the Entropy of Macromolecular Systems by Computer Simulation. T. P. Ly brand, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1990, Vol. 1, pp. 295-320. Computer Simulation of Biomolecular Systems Using Molecular Dynamics and Free Energy Perturbation Methods. 

The CHARMM (Chemistry at HARvard Macromolecular Mechanics) force field is designed for the modelling (both molecular mechanics and dynamics calculations) of macromolecular systems [67]. A revision for carbohydrates was made by Ha et al. [40]. Kouwijzer and Grootenhuis [68-69] redeveloped the CHEAT force field a CHARMm-based force field for carbohydrates with which a molecule in aqueous solution is mimicked by a simulation of the isolated molecule. 

A widely used type of multiscale simulation combines quantum mechanical and molecular mechanical (QM/MM) simulations. In this approach, the functional core of the molecular system, for example, the catalytic sites of an enzyme, is described at the electronic level (QM region), whereas the surrounding macromolecular system is treated using a classical description (MM region). Some of the biological applications for which QM/MM calculations have been widely utilized are chemical reactions in enzymes, proton transfer in proteins and optical excitations. In QM/MM... 

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