MOLECULAR GRAPHIC SIMULATION

B. R. Brooks and co-wotkets. Molecular Graphics and Simulation Laboratory, NIH, Bethesda, Md., private communication, Aug. 1991. 

Fig. 11. The sealed lip of a PCNT heat treated at 2800°C with a toroidal structure (T) and, (b) molecular graphics images of archetypal flattened toroidal model at different orientations and the corresponding simulated TEM images.

Fig. 6. above) Molecular graphics images of an archetypal flattened toroidal model of a nanotube with n = 5 and m = 4 at three different orientations (0, 5, 10, 15°) in a plane perpendicular to the paper, below) Resulting simulated TEM images of the nanotube at the above orientations to the electron beam note that even the spring onion-like bulges at the ends are reproduced. 

The adsorption of the modifier-substrate complex onto Pt (111) surface was investigated using the Soiids-Docking module of the Insightll package. This module determines the conformations of the adsorbed molecules by a combined approach of high temperature molecular dynanuc simulations with molecular mechanics minimization. All the calculated structures were visualized on a Silicon Graphics workstation. 

Tapia, O., Paulino, M. and Stamato, F. M. L. G. Computer assisted simulations and molecular graphics methods in molecular design. 1.Theory and applications to enzyme active-site directed drug design,... 

Another major advantage of molecular graphics is that it allows real time manipulation of several interacting molecules while quantitatively monitoring the stereochemistry and even the interaction energies. These methods are only beginning to be used for studies of interactions between molecules and only in the most preliminary way for the simulation of protein adsorption 29). 

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. 

Fig. 29. Computer simulated molecular graphics (wireframe) using POLYGRAF for STAR-BURST (polyether) dendrimers of generations 1-4...

Einally, we draw attention to several review articles in this area. In 1986 Lowdin 23 considered various aspects of the historical development of computational QC in view of the development of both conventional supercomputers and large-scale parallel computers. More recently, Weineri24 presented a discussion on the programming of parallel computers and their use in molecular dynamics simulations, free energy perturbation, and large scale ab initio calculations, as well as the use of very elaborate graphical display programs in chemistry research. We also note a review on the use of parallel processors in... 

As part of their efforts to employ parallel computers for molecular dynamics simulations, Schulten and co-workers generated a series of MD benchmarks based on their own program on a wide range of machines, including an Apple Macintosh II, a Silicon Graphics 320 VGX, a 32K-processor Conneaion Machine CM-200, a 60-node INMOS Transputer system, and a network of Sun workstations (using Linda).2 8 j e benchmarks demonstrated that the program runs very efficiently on many platforms (e.g., at sevenfold Cray 2 processor speed on the CM-200 and at Cray 2 processor speed on the Transputer system). 

Monte Carlo and molecular dynamics simulations on polymers. Silicon Graphics, Hewlett-Packard, and IBM RS/6000. 

Tel. 617-873-2669, fax 617-873-3776, e-mail prophet-info bbn.com Molecular building, molecular mechanics, simulations, and graphics. Statistical and mathematical modeling and display. Sequence analysis. Structural and sequence database retrieval. UNIX workstations, such as Sun, VAX (Ultrix), DECstations, and Macintosh (A/UX). 

W. Smith and T. R. Forester, J. Mol. Graphics, 14, 136 (1996). DL Poly 2.0—A General Purpose Parallel Molecular Dynamics Simulation Package. 

Molecular Mechanics Simulations of Ligand Structures in Transition Metal Carbonyl Clusters. ROTOCHEM— A Molecular Graphics Program. ... 

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