Macromolecular simulations

Elamrani et al. 1996] Elamrani, S., Berry, M.B., Phillips Jr., G.N., McCammon, J.A. Study of Global Motions in Proteins by Weighted Masses Molecular Dynamics Adenylate Kinase as a Test Case. Proteins 25 (1996) 79-88 [Elcock et al. 1997] Elcock, A.H., Potter, M.J., McCammon, J.A. Application of Poisson-Boltzmann Solvation Forces to Macromolecular Simulations. In Computer Simulation of Biomoleeular Systems, Vol. 3, A.J. Wilkinson et al. eds., ESCOM Science Publishers B.V., Leiden... 

W. Smith and T. R. Forester, Parallel macromolecular simulations and the replicated data strategy . Comp. Phys. Comm., Vol 79, no 1, 52-62, 1994. 

Ewald summation has been applied successfully for many years to liquid simulations [35] and is now becoming a standard for macromolecular simulations [36]. For this reason we focus on Ewald summation for the remainder of this section. 

Ota, N. Brunger, A.T., Overcoming barriers in macromolecular simulations non-Boltzmann thermodynamic integration, Theor. Chem. Acc. 1997, 98, 171-181... 

Tsui V, Case DA (2001) Theory and applications of the generalized Born solvation model in macromolecular simulations, Biopolymers, 56 275-291... 

Finally, we draw attention to a parallel macromolecular simulation package, DL POLY, currently under development, which incorporates many of the parallel developments of Smith and co-workers. 

W. Smith and T. R. Forester, Daresbury Laboratory Preprint DL/SCI/P873T Warrington, U.K., 1993. Parallel Macromolecular Simulations and the Replicated Data Strategy. I. The Computation of Atomic Forces. 

P. J. Steinbach and B. R. Brooks, New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation, J. Comput. Chem., 15 (1994), 667-683. 

Session Chairman and Discussion Leader Macromolecular Simulations. ... 

W. Huisinga and B. Schmidt (2005) Metastability and dominant eigenvalues of transfer operators. In New Algorithms for Macromolecular Simulation (C. Chipot, R. Fiber, A. Laaksonen, B. Leimkuhler, A. Mark, T. Schlick, C. Schiitte, and R. Skeel, eds.), vol. 49 of Lecture Notes in Computational Science and Engineering, Springer, to appear... 

It is possible to eliminate all mass effects and all dynamical information in determining the ensemble averages by the use of Monte Carlo simulation procedures. The direct application of such fully stochastic techniques is not common in the field of macromolecular simulations because the presence of... 

A second application of the index is its use to predict candidate molecules to fill molecular cavities. With the increasing use of molecular graphics, the fit, docking, or intercalation of molecules into cavities in macromolecular simulations becomes an important consideration in drug design. The visualizations of proposed receptor sites, enzyme active sites, and other cavities and spaces of interest in macromolecules make it possible to make measurements of the dimensions of a cavity. Of course, the validity of these images depends on the quality of the input data and the assumptions attending the calculations. If the visualized details of a cavity are to be believed, then there is certainly some interest in what molecules may fit that cavity or some part of it. 

For condensed-phase and macromolecular simulations, we have written an X-Pol software package using the C-p-p language, which has been incorporated into NAMD and CHARMM. The X-Pol program can be used with the popular NDDO-based semiempirical Hamiltonians as well as the recently developed polarized molecular orbital (PMO) model. - Molecular d3mamics simulations of liquid water have been carried out using the NAMD/X-Pol interface. In addition, we have used an earlier version of the X-Pol model in Monte Carlo simulations of liquid water. 

Sherwood P, Brooks BR, Sansom MSP (2008) Multiscale methods for macromolecular simulations. Curr Opin Stmct Biol 18 630-640... 

Generalized Born Solvation Model in Macromolecular Simulations. 

R. D. MacElroy, Y. Coekelenbergh, and R. Rein (1977), Macromolecular simulations as an approach to the study of the origins of self-replicating systems. Biosystems 9, 111-119. 

Sherwood, R, Brooks, B. R., 8c Sansom, M. S. (2008). Multiscale methods for macromolecular simulations. Current Opinion in Structural Biology, 1, 630. 

In the field of macromolecular simulation, the coarsegrained (CG) method, based on a viewpoint that the phase behaviors of various polymers depend on a few parameters and not sensitively on the details of molecular structures, is often used. The general property of phase separation only depends on the chain length and Flory interaction in the mean field. For example, the transition point of phase separation for the symmetric diblock copolymer is /A 10.5 [12]. A specific polymer chain can be represented using different CG models. For example, a polystyrene-fc-polyethyleneoxide (PS- -PEO) chain can be represented using lattice model, off-lattice model, or even string model (Fig. 15.2). 

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