Next: Index
Up: NAMD 2.6 User's Guide
Previous: Documentation
Contents
Index
- 1
-
M. P. Allen and D. J. Tildesley.
Computer Simulation of Liquids.
Oxford University Press, New York, 1987.
- 2
-
P. H. Axelsen and D. Li.
Improved convergence in dual-topology free energy calculations
through use of harmonic restraints.
J. Comput. Chem., 19:1278-1283, 1998.
- 3
-
F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, J. E. F. Meyer, M. D. Brice,
J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi.
The protein data bank: A computer-based archival file for
macromolecular structures.
J. Mol. Biol., 112:535-542, 1977.
- 4
-
D. L. Beveridge and F. M. DiCapua.
Free energy via molecular simulation: Applications to chemical and
biomolecular systems.
Annu. Rev. Biophys. Biophys., 18:431-492, 1989.
- 5
-
S. Boresch and M. Karplus.
The role of bonded terms in free energy simulations: I. theoretical
analysis.
J. Phys. Chem. A, 103:103-118, 1999.
- 6
-
B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan,
and M. Karplus.
CHARMM: a program for macromolecular energy, minimization, and
dynamics calculations.
J. Comp. Chem., 4(2):187-217, 1983.
- 7
-
A. T. Brünger.
X-PLOR, Version 3.1, A System for X-ray Crystallography and
NMR.
The Howard Hughes Medical Institute and Department of Molecular
Biophysics and Biochemistry, Yale University, 1992.
- 8
-
D. Chandler.
Introduction to modern statistical mechanics.
Oxford University Press, 1987.
- 9
-
C. Chipot and D. A. Pearlman.
Free energy calculations. the long and winding gilded road.
Mol. Sim., 28:1-12, 2002.
- 10
-
C. Chipot and A. Pohorille, editors.
Free energy calculations. Theory and applications in chemistry
and biology.
Springer Verlag, 2007.
- 11
-
E. Darve and A. Pohorille.
Calculating free energies using average force.
J. Chem. Phys., 115:9169-9183, 2001.
- 12
-
W. K. den Otter and W. J. Briels.
Free energy from molecular dynamics with multiple constraints.
Mol. Phys., 98:773-781, 2000.
- 13
-
J. Gao, K. Kuczera, B. Tidor, and M. Karplus.
Hidden thermodynamics of mutant proteins: A molecular dynamics
analysis.
Science, 244:1069-1072, 1989.
- 14
-
M. K. Gilson, J. A. Given, B. L. Bush, and J. A. McCammon.
The statistical-thermodynamic basis for computation of binding
affinities: A critical review.
Biophys. J., 72:1047-1069, 1997.
- 15
-
J. Hénin and C. Chipot.
Overcoming free energy barriers using unconstrained molecular
dynamics simulations.
J. Chem. Phys., 121:2904-2914, 2004.
- 16
-
W. Humphrey and A. Dalke.
VMD user guide (Version 0.94).
Beckman Institute Technical Report TB-94-07, University of Illinois,
1994.
- 17
-
P. M. King.
Free energy via molecular simulation: A primer.
In W. F. Van Gunsteren, P. K. Weiner, and A. J. Wilkinson, editors,
Computer simulation of biomolecular systems: Theoretical and
experimental applications, volume 2, pages 267-314. ESCOM, Leiden, 1993.
- 18
-
J. G. Kirkwood.
Statistical mechanics of fluid mixtures.
J. Chem. Phys., 3:300-313, 1935.
- 19
-
P. A. Kollman.
Free energy calculations: Applications to chemical and biochemical
phenomena.
Chem. Rev., 93:2395-2417, 1993.
- 20
-
N. Lu, D. A. Kofke, and T. B. Woolf.
Improving the efficiency and reliability of free energy perturbation
calculations using overlap sampling methods.
J. Comput. Chem., 25:28-39, 2004.
- 21
-
A. E. Mark.
Free energy perturbation calculations.
In P. v. R. Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A.
Kollman, H. F. Schaefer III, and P. R. Schreiner, editors, Encyclopedia
of computational chemistry, volume 2, pages 1070-1083. Wiley and Sons,
Chichester, 1998.
- 22
-
J. A. McCammon and S. C. Harvey.
Dynamics of Proteins and Nucleic Acids.
Cambridge University Press, Cambridge, 1987.
- 23
-
D. A. Pearlman.
A comparison of alternative approaches to free energy calculations.
J. Phys. Chem., 98:1487-1493, 1994.
- 24
-
D. Rodriguez-Gomez, E. Darve, and A. Pohorille.
Assessing the efficiency of free energy calculation methods.
J. Chem. Phys., 120:3563-3578, 2004.
- 25
-
A. Roitberg and R. Elber.
Modeling side chains in peptides and proteins: Application of the
locally enhanced sampling technique and the simulated annealing methods to
find minimum energy conformations.
95:9277-9287, 1991.
- 26
-
C. Simmerling, T. Fox, and P. A. Kollman.
Use of locally enhanced sampling in free energy calculations:
Testing and application to the
anomerization of
glucose.
120(23):5771-5782, 1998.
- 27
-
C. Simmerling, M. R. Lee, A. R. Ortiz, A. Kolinski, J. Skolnick, and P. A.
Kollman.
Combining MONSSTER and LES/PME to predict protein structure from
amino acid sequence: Application to the small protein CMTI-1.
122(35):8392-8402, 2000.
- 28
-
M. Sprik and G. Cicotti.
Free energy from constrained molecular dynamics.
J. Chem. Phys., 109:7737-7744, 1998.
- 29
-
T. P. Straatsma and J. A. McCammon.
Computational alchemy.
Annu. Rev. Phys. Chem., 43:407-435, 1992.
- 30
-
G. M. Torrie and J. P. Valleau.
Nonphysical sampling distributions in monte carlo free energy
estimation: Umbrella sampling.
J. Comput. Phys., 23:187-199, 1977.
- 31
-
W. F. van Gunsteren.
Methods for calculation of free energies and binding constants:
Successes and problems.
In W. F. Van Gunsteren and P. K. Weiner, editors, Computer
simulation of biomolecular systems: Theoretical and experimental
applications, pages 27-59. Escom, The Netherlands, 1989.
- 32
-
R. W. Zwanzig.
High-temperature equation of state by a perturbation method. i.
nonpolar gases.
J. Chem. Phys., 22:1420-1426, 1954.
namd@ks.uiuc.edu