Free energy perturbation calculation

Chipot, C. Kollman, P. A. Pearlman, D. A., Alternative approaches to potential of mean force calculations free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions, J. Comput. Chem. 1996,17, 1112-1131... 

C. Chipot, P. A. Kollman, and D. A. Pearlman,/. Comput. Chem., 17,1112 (1996). Alternative Approaches to Potential of Mean Force Calculations Free Energy Perturbation Versus Thermodynamic Integration Case Study of Some Representative Nonpolar Interactions. 

Perturbation theory is also used to calculate free energy differences between distinct systems by computer simulation. This computational alchemy is accomplished by the use of a switching parameter X, ranging from zero to one, that transfonns tire Hamiltonian of one system to the other. The linear relation... 

Wesolowski T A and Warshel A 1994 Ab initio free energy perturbation calculations of solvation free energy using the frozen density functional approach J. Phys. Chem. 98 5183... 

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. 

Mark, A.E. Free energy perturbation calculations. Encyclopaedia of Computational Chemistry, Wiley, New York, (1998) (in press). 

Calculations of relative partition coefficients have been reported using the free energy perturbation method with the molecular dynamics and Monte Carlo simulation methods. For example, Essex, Reynolds and Richards calculated the difference in partition coefficients of methanol and ethanol partitioned between water and carbon tetrachloride with molecular dynamics sampling [Essex et al. 1989]. The results agreed remarkably well with experiment... 

Miyamoto S and P A Kollman 1993a. Absolute and Relative Binding Tree Energy Calculations of the Interaction of Biotin and its Analogues with Streptavidin Using Molecular Dynamics/Free Energy Perturbation Approaches. Proteins Structure, Function and Genetics 16 226-245. 

Pearlman D A and P A Kollman 1989. A New Method for Carrying Out Free-Energy Perturbation Calculations - Dynamically Modified Wmdows. Journal Of Chemical Physics 90 2460-2470. 

S Hirono, PA Kollman. Calculation of the relative binding free energy of 2 -GMP and 2 -AMP to ribonuclease T1 using molecular dynamics/free energy perturbation approaches. J Mol Biol 212 197-209, 1990. 

CALCULATION OF SOLVATION ENERGIES BY FREE-ENERGY PERTURBATION METHODS... 

FIGURE 3.2. A free-energy perturbation calculation of the free energy associated with an adiabatic charging of an Na+ ion in water (Ref. 10). The parameter A transforms the solute from it uncharged (A = 0) to its charged form (A = 1). 

An area of development is the inclusion of code necessary for free energy perturbation calculations for internal, van der Waals and electrostatic energy terms ( ). Another area of development is the option to use lookup tables for both nonbond energies and for constraint energy terms such as a solvent boundary energy term (16). Other features and options are routinely added as needed to aid in the execution of current projects underway within the NIH. 

One weakness of this treatment, however, is that it neglects entropic contributions. Entropic contributions were considered in the free energy profiles (FEP) calculated earlier using umbrella sampling [58] and Monte Carlo Free energy Perturbation [59], both using a QM/MM scheme and the AMI Hamiltonian for the QM part. Our group used the same SIESTA DFT-based QM/MM method described above... 

Riccardi D, Schaefer P, Cui Q (2005) pKa Calculations in Solution and Proteins with QM/MM Free Energy Perturbation Simulations A Quantitative Test of QM/MM Protocols. J Phys Chem B 109 17715-17733. 

Wesolowski, T. A. and A. Warshel. 1994. Ab initio Free Energy Perturbation Calculations of Solvation Free Energy Using Frozen Density Functional Approach. J. Phys. Chem. 98, 5183. 

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