Bio-molecular simulation

Mahoney MW, Jorgensen WL. A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolar-izable potential functions. J. Chem. Phys. 2000 112 8910-8922. Rick SW. A reoptimization of the five-site water potential TIP5P for use with Ewald sums. J. Chem. Phys. 2004 120 6085-6093. Horn HW, Swope WC, Pitera JW, Madura JD, Dick TJ, Hura GL, Head-Gordon T. Development of an improved four-site water model for bio-molecular simulations UP4P-Ew. J. Chem. Phys. 2004 120 9665-9678. 

It is clear from the data in Table 3 that first-order sensitivity theory works best when e. and Ae, are both small. When e. and Ae, are of the order of 2 k, the predictive reliability decreased to 75%. Therefore, first-order sensitivity theory does not always give correct predictions. However, since first-order sensitivity coefficients can usually be calculated more easily than higher order sensitivity coefficients in (bio)molecular simulations, first-order sensitivity coefficients can be used as a preliminary screening tool for suggesting a small number of modifications to a (bio)molecule that may lead to the desired biological effect. More sophisticated (but usually more expensive) calculations and/or suitable experimental studies can then be carried out to sort out from this small number of suggestions those that are more likely to achieve the desired biological effects. If experimentation is easier, the predictions can be tested in the laboratory. 

Sensitivity analysis is also a tool that can help to refine potential energy functions for (bio)molecular simulations. Sensitivity analysis can help one decide whether a specific feature needs to be included in a potential function for describing a specified set of properties of a given class of molecules. For example, because point charge models are commonly used in bio(molecular) modeling, it is useful to inquire whether a dispersed charge representation would improve the description of intra- and intermolecular electrostatic interactions. One study of this type was carried out by Zhu and Wong," ° who included in the force field a squared Lorentzian function f r - f/ ) of the form... 

This paper also provided much of the early stimulus for developing semiclassical and quantum mechanical theories of chemical reaction dynamics, which is a research field that continues to be active. In addition, this paper provided the foundation for molecular dynamics studies of chemical reactions in condensed phases, including applications to gas-surface scattering and bio-molecular simulation. 

Voth, G. A., Computer simulation of proton solvation and transport in aqueous and bio-molecular systems, Acc. Chem. Res. 2006, 39, 143-150. 

Molecular simulations have been used for more than the past 50 years to observe properties of bio-molecules, organic, and inorganic compounds in their natural... 

Abstract In order to model (bio)molecular systems and to simulate their dynamics one requires... 

Summary. In conclusion, the advent of current generation computers has allowed the development of a new level of rigor in statistical thermodynamic and dynamic studies of organic and bio-molecular systems. We have discussed how we can now include the relaxation of molecular geometry, the treatment of conformational entropy, and the inclusion of solvent effects in theoretical treatments of biolmolecular systems, all of extreme importance in simulating the behavior of those systems. In addition we have indicated how the vibrational spectra can be calculated and its conformational dependence be used as a probe of conformation. It was pointed out that these developments have for the most part occurred within the last five years and in fact most publications in the area have been in the last year or two. Their full Impact on this exciting field is yet to be felt. 

T. P. Lybrand, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1990, Vol. 1, pp. 295-320. Computer Simulation of Bio-molecular Systems Using Molecular Dynamics and Free Energy Perturbation Methods. 

Polarizable Continuum Models for (Bio)Molecular Electrostatics Basic Theory and Recent Developments for Macromolecules and Simulations... 

With this book, our goal is to not only provide an up-to-date snapshot of the current molecular simulation field but also stimulate the exchange of ideas across different sub-fields of modern computational (bio)chemistry. We hope that the book will... 

W.E. van Gunsteren and P.K. Weiner, Computer Simulations of Bio-molecular Systems. Theoretical and Experimental Applications. 

MD simulations provide a complete atomistic view of (bio-)molecular motions on the femtosecond to microsecond scale. The free energy landseape determines which states will contribute to an ensemble of structures at a given temperature. Also kinetic aspects, e g., transition frequencies between different states are determined by the energy barriers within the free energy landscape of the system [12]. Molecular dynamics simrrlations explore the landscape given an energy distribution determined by the system s temperature. 

Latour, R. A. (2008). Molecular simulation of protein-surface interactions benefits, problems, solutions, and future directions. Bio interphases, 3, FC2-FC12. http //dx.doi.org/10.1116/L2965132. 

This section briefly mentions two practical aspects related to the use of thermostats in MD simulations of (bio-)molecular systems. 

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