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  • 1
    Electronic Resource
    Electronic Resource
    Solution Structure of FK506 Bound to the R42K, H87V Double Mutant of FKBP-12 (1994)
    s.l. : American Chemical Society
    Biochemistry 33 (1994), S. 13571-13580 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00250a009
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  • 2
    Electronic Resource
    Electronic Resource
    Evaluating the assumptions underlying force field development and application using free energy conformational maps for nucleosides (1991)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 113 (1991), S. 7167-7177 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00019a012
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  • 3
    Electronic Resource
    Electronic Resource
    Simulation of the solvation free energies for methane, ethane, and propane and corresponding amino acid dipeptides: a critical test of the bond-PMF correction, a new set of hydrocarbon parameters, and the gas phase-water hydrophobicity scale (1992)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 114 (1992), S. 6798-6801 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00043a027
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  • 4
    Electronic Resource
    Electronic Resource
    The overlooked bond-stretching contribution in free energy perturbation calculations (1991)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 94 (1991), S. 4532-4545 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We examine the validity of an assumption commonly made when carrying out free energy perturbation (FEP) calculations: The contributions to the free energy difference from intraperturbed group interactions are negligible. We show: (A) that these contributions are not, in fact, necessarily negligible; and (B) that, in particular, the bond-stretching contribution resulting from changes in equilibrium bond lengths is important, but can be extremely difficult to calculate using standard procedures. We show how this contribution can be determined using an alternative "pseudopotential of mean force'' correction. We also examine the behavior of the calculated free energy with the length of the simulation, and conclude that simulation times significantly longer than those typically used at present (e.g., ≥200 ps) may be required to yield reliable and accurate results.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.460608
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  • 5
    Electronic Resource
    Electronic Resource
    The lag between the Hamiltonian and the system configuration in free energy perturbation calculations (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 7831-7839 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The energetic response of two test systems to changes in the governing Hamiltonians (empirical potential energy functions) are examined. For these two systems—neon in water using periodic boundary conditions and partially solvated trypsin—a systematic lag is observed between changes in the Hamiltonian and changes in a component of the energetic trajectory which is relevant to free energy perturbation (FEP) calculations. This observation appears inconsistent with one of the underlying assumptions of a commonly used implementation of FEP simulations: "slow growth'' or "thermodynamic integration.'' The calculations presented here suggest that the relevant component of the system energetics lags the Hamiltonian by a minimum of about 0.6 ps. Implications of this lag for designing reliable methodologies to use with various implementations of FEP calculations are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.457251
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  • 6
    Electronic Resource
    Electronic Resource
    A new method for carrying out free energy perturbation calculations: Dynamically modified windows (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 90 (1989), S. 2460-2470 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new methodology for carrying out free energy perturbation calculations is derived and implemented in an extensively modified version of the amber 3.0 program (U. C. Singh, P. K. Weiner, J. W. Caldwell, and P. A. Kollman, Department of Pharmaceutical Chemistry, University of California, San Francisco, 1986). In this method, the local slope of the accumulated free energy vs λ curve is used to choose the width, δλ of the next window. This method has been evaluated on several test cases: the free energies of solvation for the noble gases neon, krypton, and xenon; and the free energy of solvation of methane. In each case, good agreement between theory and experiment is obtained in a reasonably short amount of simulation time using the new methodology. In contrast, when these test cases are run using a standard fixed δλ methodology for the same lengths of time, much worse results are obtained. This attests to the ability of the new method to reduce the radius of convergence for these types of free energy calculations.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.455988
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  • 7
    Electronic Resource
    Electronic Resource
    Walking on the free energy hypersurface of the 18-crown-6 ion system using free energy derivatives (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 101 (1994), S. 627-633 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Molecular dynamics simulations have been used to calculate free energy derivatives with respect to nonbonded parameters for both ions and the host, 18-crown-6 in cation-18-crown-6 complexes. The free energy derivatives have been used to examine the free energy hypersurface for such complexes and to "predict'' the optimal cationic ligand for 18-crown-6 complexation in aqueous solution. This method has promise to enable the refinement of the intermolecular interaction parameters for both hosts and guests in aqueous solution. In particular, we show that the optimal ion size for 18-crown-6 is calculated to be between the sizes of Na+ and K+, consistent with the experimental data. More generally, it has potential to be a powerful tool in computer aided molecular design.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.468117
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  • 8
    Electronic Resource
    Electronic Resource
    A Comparison of Alternative Approaches to Free Energy Calculations (1994)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 98 (1994), S. 1487-1493 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j100056a020
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  • 9
    Electronic Resource
    Electronic Resource
    Determining the contributions of constraints in free energy calculations: Development, characterization, and recommendations (1993)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 98 (1993), S. 8946-8957 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We develop and/or characterize three methods for determining the contributions of constraints in free energy calculations. A new method for determining such contributions in thermodynamic integration (TI) calculations, the potential forces (PF) method, is developed and compared to a second method, the constraint forces (CF) method. Both methods are also compared to a previously described technique for calculating such contributions in free energy perturbation (FEP) simulations. We find that the TI/PF protocol is considerably more efficient than the TI/CF method, and is preferred except in cases where the constraints contributing to the free energy are part of a closed ring. Compared to TI/PF, the FEP method is shown to be relatively poor for generating potential of mean force (PMF) curves, though the FEP method is suitable for determining the "PMF bond contribution'' in compositional free energy changes. PMF curves for a system of two neon atoms in a periodic box of water have been derived. The convergence behavior of the free energy derivative ∂G/∂R, where R is a distance constraint, has been examined in detail for this system. As much as a nanosecond of molecular dynamics sampling can be required to derive a fully converged value for this derivative at a single (λ) point. We have determined the sampling ratio for ∂G/∂R as a function of Ne–Ne distance for a 295 water (21 A(ring)/side) periodic water box, and conclude that for free energy changes where long-distance constraint contributions are being determined, a minimum of 0.7 ps of sampling should be performed per window. When constraint contributions arise from short distances (such as when the PMF bond contribution is being calculated), correlation in the constraint derivative series dies out relatively quickly and the minimum sampling—then dictated by correlation in the nonbonded series—should be about 0.6 ps.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.464453
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  • 10
    Electronic Resource
    Electronic Resource
    Calculations of the relative free energies of aqueous solvation of several fluorocarbons: A test of the bond potential of mean force correction (1993)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 99 (1993), S. 9103-9110 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The relative free energies of aqueous solvation of several fluorinated derivatives of methane were calculated using the free energy perturbation (FEP) method. The calculations in general duplicated the experimental free energies with relatively good accuracy, but the calculation of the bond potential of mean force (bond-PMF) contribution [D. A. Pearlman and P. A. Kollman, J. Chem. Phys. 94, 4532 (1991)] was necessary in order to get the most satisfactory agreement with experiment. In particular, it was necessary to use this contribution to obtain even qualitatively correct results for the relative free energies of hydration of methane and tetrafluoromethane. The reasons for this are discussed in terms of the accurate calculation of the effect of the size of the solute. In addition, it is noted that the bond-PMF contribution is important even for FEP calculations not involving large changes in size, such as the ethanol to ethane perturbation, if the length of a bond to a disappearing atom is changed during the perturbation. The relative free energy of aqueous solvation for ethanol and ethane was calculated to demonstrate that if the bond between the oxygen and the hydroxyl hydrogen being removed is "shrunken'' during the perturbation without including the bond-PMF correction, the calculated free energy is too low by ∼3 kcal/mol.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.465525
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