Suggested introductory references

The papers listed here emphasize the theory and experience with the AMBER programs; beyond listing "general reviews", we have not attempted to list the many other papers that would be relevant to the field.

1. D.L. Beveridge and F.M. Di Capua (1989) "Free Energy Via Molecular Simulation: Applications to Chemical and Biomolecular Systems." Annu. Rev. Biophys. Biophys. 18, 431-492.
2. P.A. Kollman (1993) "Free Energy Calculations: Applications to Chemical and Biochemical Phenomena." Chem. Rev. 93, 2395-2417.

1. D.A. Pearlman and P.A. Kollman (1989) "Free Energy Perturbation Calculations: Problems and Pitfalls Along the Gilded Road." In: Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications (W. van Gunsteren and P.K. Weiner, eds.), pp. 101-119, Escom Science Publishers, Netherlands.
2. W.F. van Gunsteren, "Methods for Calculation of Free Energies and Binding Constants: Successes and Problems," ibid, pp.27-59.
3. D.A. Pearlman and P.A. Kollman (1989) "The Lag Between the Hamiltonian and the System Configuration in Free Energy Perturbation Calculations." J. Chem. Phys. 91, 7831-7839.
4. D.A. Pearlman and P.A. Kollman (1991) "The Overlooked Bond-Stretching Contribution in Free Energy Perturbation Calculations." J. Chem. Phys. 94, 4532-4545.
5. D.A. Pearlman (1994) "Free energy derivatives: A new method for probing the convergence problem in free energy calculations.", J. Comp. Chem. 15, 105-123.
6. D.A. Pearlman (1994) "A comparison of alternative approaches to free energy calculations.", J. Phys. Chem. 98, 1487-1493.
7. R.J. Radmer and P.A. Kollman (1997) "Free energy calculation methods: A theoretical and empirical comparison of numerical errors and a new method for qualitative estimates of free energy changes." J. Comp. Chem. 18, 902-919.

1. D.A.Pearlman and P.R. Connely (1995) "Deterimation of the Differential Effects of Hydrogen Bonding and Water Release on the Binding of FK506 to Native and Y82F FKBP-12 Proteins Using Free Energy Simulations.", J. Mol. Biol. 148, 696-171.
2. J.L. Miller and P.A.Kollman, (1996) "Solvation Freen Energies of the Nulceic Acid Bases.", J. Phys. Chem. 100, 8587-8594.
3. E.C. Meng, J.W. Caldwell, and P.A. Kollman, (1996) "Investigating the Anomalous Solvations Free Energies of Amines with a Polariazable Potential.", J. Phys. Chem. 100, 2367-2371.

1. D.A. Pearlman and P.A. Kollman (1989) "A New Method for Carrying Out Free Energy Perturbation Calculations: Dynamically Modified Windows." J. Chem. Phys. 90, 2460-2470.

1. D.J. Tobias and C.L. Brooks, III (1988) "Molecular Dynamics with Internal Coordinate Constraints." J. Chem. Phys. 89, 5115-5127.
2. D.A. Pearlman (1993) "Determining the contributions of constraints in free energy calculations: Development, characterization, and recommendations", J. Chem. Phys. 98, 8946-8957.

1. D.A. Pearlman and P.A. Kollman (1991) "Evaluating the Assumptions Underlying Force Field Development and Application, Using Free Energy Conformational Maps for Nucleosides." J. Am. Chem. Soc. 113, 7167-7177.
2. C. Chipot, P.A. Kollman and D.A. Pearlman (1996) "Alternative approaches to potential of mean force calculations: free energy pertubation versus thermodynamics integration. Case study of some representative nonpolar interactions", J. Comp. Chem. 17, 1112-1131.

   In addition, it is strongly suggested that the user read the discussion which follows the description of the input variables before using GIBBS.