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Free energy calculating

Jorgenson W 1989 Free energy calculations a breakthrough in modeling organic chemistry in solution Accounts Chem. Res. 22 184... [Pg.555]

Reynolds C, King P M and Richards W G 1992 Free energy calculations in molecular biophysics Mol. Phys. 76 251... [Pg.558]

We assume that the unbinding reaction takes place on a time scale long ( ompared to the relaxation times of all other degrees of freedom of the system, so that the friction coefficient can be considered independent of time. This condition is difficult to satisfy on the time scales achievable in MD simulations. It is, however, the most favorable case for the reconstruction of energy landscapes without the assumption of thermodynamic reversibility, which is central in the majority of established methods for calculating free energies from simulations (McCammon and Harvey, 1987 Elber, 1996) (for applications and discussion of free energy calculation methods see also the chapters by Helms and McCammon, Hermans et al., and Mark et al. in this volume). [Pg.55]

S. Miyamoto and P. A. Kollman. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches. Proteins, 16 226-245, 1993. [Pg.96]

A linear dependence approximately describes the results in a range of extraction times between 1 ps and 50 ps, and this extrapolates to a value of Ws not far from that observed for the 100 ps extractions. However, for the simulations with extraction times, tg > 50 ps, the work decreases more rapidly with l/tg, which indicates that the 100 ps extractions still have a significant frictional contribution. As additional evidence for this, we cite the statistical error in the set of extractions from different starting points (Fig. 2). As was shown by one of us in the context of free energy calculations[12], and more recently again by others specifically for the extraction process [1], the statistical error in the work and the frictional component of the work, Wp are related. For a simple system obeying the Fokker-Planck equation, both friction and mean square deviation are proportional to the rate, and... [Pg.144]

Hermans, J., Yun, R. H., Anderson, A. G. Precision of free-energies calculated by molecular dynamics simulations of peptides in solution. J. Comp. Chem. 13 (1992) 429-442... [Pg.146]

Vorobjev, Y., Almagro, J. C., Hermans, J. Conformational free energy calculated by a new iiK thod from dynamics simulation and continuum dielectric... [Pg.147]

Radmer, R.. 1., Kollman, P. A. Approximate free energy calculation methods and structiire based ligand design. J. Comp. Aid. Mol. Desgn (in press)... [Pg.161]

Amadei, A., Apol, M. E. F., Di Nola, A., Berendsen, H. J. C. The quasi-Gaussian entropy theory Free energy calculations based on the potential energy distribution function. J. Chem. Phys. 104 (1996) 1560-1574... [Pg.162]

Beutler, T. C., Mark, A. E., van Schaik, R. C., Gerber, P. R., van Gunsteren, W. F. Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations. Chem. Phys. Letters 222 (1994) 529-539... [Pg.162]

Potential Pitfalls with Free Energy Calculations... [Pg.593]

Kollman P A 1993. Free Energy Calculations Applications to Chemical and Bicx hemica] Phenojne. Chemical Reviews 93 23 -2417. [Pg.649]

Buetler T C, A E Mark, R C van Schaik, P R Gerber and W F van Gunsteren 1994. Avoiding Singularities and Numerical Instabilities in Free Energy Calculations Based on Molecular Simulations. Chemical Physics Letters 222 529-539. [Pg.650]

Burger M T, A Armstrong, F Guamieri, D Q McDonald and W C Still 1994. Free Energy Calculations in Molecular Design Predictions by Theory and Reality by Experiment with Enantioselective Podand lonophores. Journal of the American Chemical Society 116 3593-3594. [Pg.650]

Eriksson M A L, J Pitera and P A Kollman 1999. Prediction of the Binding Free Energies of New TIBO-like HIV-1 Reverse Transcriptase Inhibitors Using a Combination of PROFEC, PB/SA, CMC/MD, and Free Energy Calculations. Journal of Medicinal Chemistry 42 868-881. [Pg.650]

Gu > Z, C L Brooks III and X Kong 1998. Efficient and Flexible Algorithm for Free Energy Calculation using the A-Dynamics Approach. Journal of Physical Chemistry B102 2032-2036. [Pg.651]


See other pages where Free energy calculating is mentioned: [Pg.2248]    [Pg.63]    [Pg.155]    [Pg.160]    [Pg.352]    [Pg.11]    [Pg.16]    [Pg.579]    [Pg.588]    [Pg.588]    [Pg.592]    [Pg.592]    [Pg.594]    [Pg.594]    [Pg.596]    [Pg.601]    [Pg.601]    [Pg.649]    [Pg.652]   
See also in sourсe #XX -- [ Pg.266 ]

See also in sourсe #XX -- [ Pg.266 ]

See also in sourсe #XX -- [ Pg.267 ]




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