Simulation, computer, 50 molecular

Procacci P, Darden T A, Paci E and Marchi M 1997 ORAC a molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions J. Comput. Chem. 18 1848-62... 

Hilbers P A J and Esselink K 1993 Parallel computing and molecular dynamics simulations Computer Simulation In Chemloal Physios /o 397 NATO ASI Series Ced M P Allen and D J Tlldesley (Dordrecht Kluwer) pp 473-95... 

It is appropriate to consider first the question of what kind of accuracy is expected from a simulation. In molecular dynamics (MD) very small perturbations to initial conditions grow exponentially in time until they completely overwhelm the trajectory itself. Hence, it is inappropriate to expect that accurate trajectories be computed for more than a short time interval. Rather it is expected only that the trajectories have the correct statistical properties, which is sensible if, for example, the initial velocities are randomly generated from a Maxwell distribution. 

P. A. J Hilbers and K. Esselink, Parallel computing and molecular dynamics simulations , Computer Simulations in Chemical Physics, Proc. of the NATO advanced study institute on new perspectives in computer simulations in chemical physics, 473-95, 1993. 

Many problems in force field investigations arise from the calculation of Coulomb interactions with fixed charges, thereby neglecting possible mutual polarization. With that obvious drawback in mind, Ulrich Sternberg developed the COSMOS (Computer Simulation of Molecular Structures) force field [30], which extends a classical molecular mechanics force field by serai-empirical charge calculation based on bond polarization theory [31, 32]. This approach has the advantage that the atomic charges depend on the three-dimensional structure of the molecule. Parts of the functional form of COSMOS were taken from the PIMM force field of Lindner et al., which combines self-consistent field theory for r-orbitals ( nr-SCF) with molecular mechanics [33, 34]. 

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. 

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. 

The simulation of molecular (or atomic) dynamics on a computer was invented by the physicist George Vineyard, working at Brookhaven National Laboratory in New York State. This laboratory, whose biography has recently been published (Crease 1999), was set up soon after World War II by a group of American universities. 

Single-event microkinetics describe the hydrocarbon conversion at molecular level. Present day analytical techniques do not allow an identification of industrial feedstocks in such detail. In addition current computational resources are not sufficient to perform simulations at molecular level for industrial feedstock conversion. These issues are addressed using the relumping methodology. 

In the case of molten salts, no obvious model based on statistical mechanics is available because the absence of solvent results in very strong pair correlation effects. It will be shown that the fundamental properties of these liquids can be described by quasi-chemical models or, alternatively, by computer simulation of molecular dynamics (MD). 

Yu HB, van Gunsteren WF (2005) Accounting for polarization in molecular simulation. Comput Phys Commun 172(2) 69—85... 

Computer simulations of confined polymers have been popular for several reasons. For one, they provide exact results for the given model. In addition, computer simulations provide molecular information that is not available from either theory or experiment. Finally, advances in computers and simulation algorithms have made reasonably large-scale simulations of polymers possible in the last decade. In this section I describe computer simulations of polymers at surfaces with an emphasis on the density profiles and conformational properties of polymers at single flat surfaces. 

To tackle these problems successfully, new concepts will be required for developing systematic modeling techniques that can describe parts of the chemical supply chain at different levels of abstraction. A specific example is the integration of molecular thermodynamics in process simulation computations. This would fulfill the objective of predicting the properties of new chemical products when designing a new manufacturing plant. However, such computations remain unachievable at the present time and probably will remain so for the next decade. The challenge is how to abstract the details and description of a complex system into a reduced dimensional space. 

P. E. Smith and W. F. van Gunsteren, Methods for the evaluation of long range electrostatic forces in computer simulation of molecular systems, in Computer Simulation of Biomolecular Systems, vol. 2, W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson, eds., Escom, Leiden (1993), pp. 315. 

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,... 

None of the methods currently used to study molecular dynamics can span the whole time range of motions of interest, from picoseconds to seconds and minutes. However, the structural resolution of a method is of equal importance. A method has to not only provide information about the existence of motions with definite velocities but also to identify what structural element is moving and what is the mechanism of motion. Computer simulation of molecular dynamics has proved to be a very important tool for the development of theories concerning times and mechanisms of motions in proteins. In this approach, the initial coordinates and forces on each atom are input into the calculations, and classical equations of motions are solved by numerical means. The lengthy duration of the calculation procedure, even with powerful modem computers, does not permit the time interval investigated to be extended beyond hundreds of picoseconds. In addition, there are strong... 

The need to reliably describe liquid systems for practical purposes as condensed matter with high mobility at a given finite temperature initiated attempts, therefore, to make use of statistical mechanical procedures in combination with molecular models taking into account structure and reactivity of all species present in a liquid and a solution, respectively. The two approaches to such a description, namely Monte Carlo (MC) simulations and molecular dynamics (MD), are still the basis for all common theoretical methods to deal with liquid systems. While MC simulations can provide mainly structural and thermodynamical data, MD simulations give also access to time-dependent processes, such as reaction dynamics and vibrational spectra, thus supplying — connected with a higher computational effort — much more insight into the properties of liquids and solutions. 

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