Molecular dynamics graphics

Molecular graphics representation ofihe paths generated by 32 hard spherical particles in the solid (left) and ht) phase. (Reproduced from Alder B J and T E Wainwright 1959. Studies in Molecular Dynamics. I. Method. Journal of Chemical Physics. 31. 459-466.)... 

TJ Oldfield. SQUID A program for the analysis and display of data from crystallography and molecular dynamics. J Mol Graphics 10 247-252, 1992. 

Humphrey, W., Dalke, A., Schulten, K. VMD-visual molecular dynamics. J. Molec. Graphics 1996, 14, 33-38. 

The BIOGRAF program was run on a Micro VAX II conmuter equipped with an Evans and Sutherland PS390 graphics terminal. The size of coal structures evaluated, and the duration of molecular dynamics runs, were limited by the available computing speed of this system (a 5000-step, 10-ps molecular dynamics run for a 1040-atom structure, with about 75,000 van der Waals interactions per step, required about 100 hours of computation). 

Over the last 10 years, all these severe limitations of the traditional molecular mechanics approach have been tackled. The appropriate use of molecular mechanics, molecular dynamics, quantum mechanics and computer graphics has given in a number of cases useful qualitative data on solvation and binding, with good agreement between theory and experiment (Kollman and Merz, 1990). 

Realistic Images Show Molecular Dynamics Chemistry is dynamic, and it is important to portray a sense of motion. Multistep graphics are used to show as accurately as possible how molecules and ions move and interact. For example, this image shows how ions at the surface of a solid become hydrated and move into solution. 

Methods based on molecular graphics, molecular mechanics, molecular dynamics, and MO calculations, used for the design of new compounds. CAMD is not equivalent to molecular modeling but rather a subdiscipline of it (see molecular modeling, molecular mechanics, molecular dynamics). 

Molecular Mechanics Molecular Modeling Molecular Dynamics Molecular Graphics ... 

The advent of high-speed computers, availability of sophisticated algorithms, and state-of-the-art computer graphics have made plausible the use of computationally intensive methods such as quantum mechanics, molecular mechanics, and molecular dynamics simulations to determine those physical and structural properties most commonly involved in molecular processes. The power of molecular modeling rests solidly on a variety of well-established scientific disciplines including computer science, theoretical chemistry, biochemistry, and biophysics. Molecular modeling has become an indispensable complementary tool for most experimental scientific research. 

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