Molecular dynamics simulation nucleic acid systems

Molecular Dynamics Simulations on Nucleic Acid Systems Using the CorneU et al. Force Field and Particle Mesh Ewald Electrostatics... 

Another very valuable tool in arsenal of theoretical investigation of biological molecules is the method of molecular dynamics simulations. This computational method describes the time dependent behaviour of the given molecular system. To date an extensive use of molecular dynamics simulations has resulted in generation of a wealth of detailed information on the fluctuations and conformational changes of proteins and nucleic acids. Such methods are now routinely used to investigate the stracture, dynamics and thermodynamics of biological molecules and their complexes [48-50, 65-71, 85]. 

Usually refers to a method of solving Newton s equations of classical mechanics numerically, in order to propagate the positions and velocities of a system of molecules forward in time and thus to explore the phase space of the system. See Molecular Dynamics and Hybrid Monte Carlo in Systems with Multiple Time Scales and Long-range Forces Reference System Propagator Algorithms Molecular Dynamics DMA Molecular Dynamics Simulations of Nucleic Acids Molecular Dynamics Studies of Lipid Bilayers and Molecular Dynamics Techniques and Applications to Proteins. 

Molecular dynamics simulations of nucleic acid systems have lead to a wealth of data summarized in this chapter. From these simulations emeige a dynamical picture which gains in sharpness and coherence with the Joint development of MD methodologies and experimental knowledge. 

Free Energy Perturbation Calculations Molecular Dynamics and Hybrid Monte Carlo in Systems with Multiple Time Scales and Long-range Forces Reference System Propagator Algorithms Molecular Dynamics DNA Molecular Dynamics Simulations of Nucleic Acids Molecular Dynamics Studies of Lipid Bilayers. 

There are basically two ways to overcome such problems. Firstly, one can thermally excite the system so that it can escape from local minima and continue to search the surrounding conformational space. This is the principle behind molecular dynamics simulations, which generate the trajectory of a molecule in time by numerically integrating Newton s equations of motion. This technique is discussed in another section of the present volume. It is also the principle behind Monte Carlo simulations, which build up a thermodynamic ensemble of molecular conformations based on their Boltzmann probabilities. Application of this approach to nucleic acids is discussed below. 

The ENCAD (energy calculations and dynamics) force field has been developed by Levitt et al. for the molecular dynamics simulations of proteins and nucleic acids in solution. It employs all-atom force field parameters. For condensed phase simulations the new three-center, flexible water model has been developed. The stress has been laid on the energy conservation effect during molecular dynamics simulations without coupling simulated systems to the thermal bath. The following expression has been used to calculate potential energy of the molecular systems ... 

VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, and lipid bilayer assemblies. It may be used to view more general molecules, as VMD can read several different structural file formats and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. 

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

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