Free energy perturbation applications

Free energy methods - Theory II MD - Free energy perturbation - Applications Continuum electrostatics Poisson-Boltzmann - Theory... 

An early application of the free energy perturbation method was the determination of t] tree energy required to create a cavity in a solvent. Postma, Berendsen and Haak determin the free energy to create a cavity (A = 1) in pure water (A = 0) using isothermal-isobai... 

In this chapter, we will examine in depth the characteristic errors of two free energy techniques and present improved methods based on a better understanding of their behavior. The two techniques examined are free energy perturbation (FEP) [2] and nonequilibrium work (NEW) based on Jarzynski s equality [3-6]. These techniques are discussed in Chaps. 2 and 5. The FEP method is one of the most popular approaches for computing free energy differences in molecular simulation see, e.g., [1, 7-10]. The recently developed NEW method, which is closely related to FEP, is gaining popularity in both simulation [11-18] and experimental applications [19-21],... 

In spite of these potential concerns, the MEHMC method is expected to be a useful tool for many applications. One task for which it might be particularly well suited is to generate a canonical ensemble of representative configurations of a bio-molecular system quickly. Such an ensemble is needed, for example, to represent the initial conditions for the ensemble of trajectories used in fast-growth free energy perturbation methods such as the one suggested by Jarzynski s identity [104] (see also Chap. 5). 

Li, G.H. Zhang, X.D. Cui, Q., Free energy perturbation calculations with combined QM/MM. Potential complications, simplifications, and applications to redox potential calculations, J. Phys. Chem. B 2003,107, 8643-8653. 

L. M. Hansen and P.A. Kollman, Free energy perturbation calculations on models of active sites Applications to adenosine deaminase inhibitors, J. Comp. Chem. 11 994 (1990). 

Lopez MA, Kollman PA (1993) Application of molecular dynamics and free energy perturbation methods to metalloporphyrin-ligand systems II CO and dioxygen bynding to myoglobin, Protein Sci, 2 1975-1986... 

The standard and often used methods to circumvent the difficulty associated with the form of Eq. (17-30) are the free-energy perturbation and thermodynamic integration methods [13,42,43], These methods are generally applicable to free-energy... 

Tel. 415-476-4637, fax 415-476-0688, e-mail pak cgl.ucsf.edu Assisted Model Building using Energy Refinement. Energy minimization, molecular dynamics, and free energy perturbation (FEP) calculations. SPASMS (San Francisco Package of Applications for the Simulation of Molecular Systems). VAX, Cray versions. 

Application of Free Energy Perturbation to Ligand Design Using the OWFEG Method. 

Singh, U. C., Brown, F. K., Bash, P. A., and Kollman, P. A. An approach to the application of free energy perturbation methods using molecular dynamics applications to the transformations of CH3OH —> CH3CH3, H3O+ —> NH4, glycine... 

---