Computation of free energy

Helvetica Chimica Acta

Volumn 85, Issue 10, 2002, Pages 3113-3129

  Van Gunsteren, Wilfred F ^a   Daura, Xavier ^b   Mark, Alan E ^c  

^a ETH ZURICH   (Switzerland)

^b UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^c UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL COMPOUNDS; COMPUTER SIMULATION; STATISTICAL MECHANICS;

MOLECULAR SIMULATION;

FREE ENERGY;

ARTICLE; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MOLECULAR MODEL; MOLECULAR SYSTEMATICS; PRIORITY JOURNAL; STATISTICS;

EID: 0036424344     PISSN: 0018019X     EISSN: None     Source Type: Journal    
DOI: 10.1002/1522-2675(200210)85:10<3113::AID-HLCA3113>3.0.CO;2-0     Document Type: Article

References (42)

1. M. Mezei, D. L. Beveridge, Ann. N. Y. Acad. Sci. 1986, 482, 1.
2. D. L. Beveridge, F. M. DiCapua. Annu. Rev. Biophys. Biophys. Chem. 1989, 18, 431.
3. W. F. van Gunsteren, in 'Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications', Eds. W. F. van Gunsteren, P. K. Weiner. ESCOM Science Publishers, Leiden, 1989. Vol. 1, pp. 27-59.
4. D. Frenkel, in 'Computer Simulation in Material Science', NATO ASI Series E205, Eds. M. Meyer, V. Pontikis, Kluwer Academic Publishers, Dordrecht, 1991, pp. 85-117.
5. T. P. Straatsma, J. A. McCammon, Annu. Rev. Phys. Chem. 1992, 43, 407.
6. P. M. King, in 'Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications', Eds. W. F. van Gunsteren. P. K. Weiner, A. J. Wilkinson, ESCOM Science Publishers, Leiden, 1993, Vol. 2. pp. 267-314.
7. W. F. van Gunsteren, T. C. Beutler, F. Fraternali, P. M. King, A. E. Mark, P. E. Smith, in 'Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications', Eds. W. F. van Gunsteren, P. K. Weiner, A. J. Wilkinson, ESCOM Science Publishers: Leiden, 1993. Vol. 2, pp. 315-348.
8. T. P. Straatsma, in 'Reviews in Computational Chemistry', Eds. K. B. Lipkowitz. D. B. Boyd. VCH Publishers, New York, 1996. Vol. 9, pp. 81-127.
9. A. E. Mark, in 'Encyclopedia of Computational Chemistry', Eds. P. von Ragué Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A. Kollman. H. F. Schaefer III, P. R. Schreiner, John Wiley & Sons, Chichester, 1998, Vol. 2, pp. 1070-1083.
10. D. A. McQuarrie, 'Statistical Mechanics'. Harper and Row, New York, 1976.
11. H. J. C. Berendsen, in 'Proteins: Structure, Dynamics and Design', Eds. V. Enugopalakrishnan, P. R. Carey, I. C. P. Smith, S. G. Huang, A. C. Storer, ESCOM Science Publishers, Leiden, 1991, pp. 384-392.
12. P. H. Hünenberger, J. K. Granwehr, J.-N. Aebischer, N. Ghoneim, E. Haselbach. W. F. van Gunsteren, J. Am. Chem. Soc. 1997, 119, 7533.
13. X. Daura, W. F. van Gunsteren, A. E. Mark. Proteins: Struct. Funct. Genet. 1999, 34, 269.
14. J. G. Kirkwood, J. Chem. Phys. 1935, 3, 300.
15. R. Zwanzig, J. Chem. Phys. 1954, 22, 1420.
16. B. Widom, J. Chem. Phys. 1963, 39, 2808.
17. P. E. Smith. W. F. van Gunsteren, J. Chem. Phys. 1994, 100, 577.
18. G. M. Torrie, J. P. Valleau, J. Comput. Phys. 1977, 23, 187.
19. A. E. Mark, W. F. van Gunsteren, J. Mol. Biol. 1994, 240, 167.
20. P. E. Smith, W. F. van Gunsteren, J. Phys. Chem. 1994, 98, 13735.
21. J. Schlitter, Chem. Phys. Lett. 1993, 215, 617.
22. H. Schäfer, A. E. Mark, W. F. van Gunsteren, J. Chem. Phys. 2000, 113, 7809.
23. H. Schäfer, X. Daura, A. E. Mark, W. F. van Gunsteren, Proteins: Struct. Funct. Genet. 2001, 43, 45.
24. H. Liu, A. E. Mark, W. F. van Gunsteren, J. Phys. Chem. 1996, 100, 9485.
25. T. C. Beutler, D. R. Béguelin, W. F. van Gunsteren, J. Chem. Phys. 1995, 102, 3787.
26. A. E. Mark, W. F. van Gunsteren, H. J. C. Berendsen, J. Chem. Phys. 1991, 94, 3808.
27. T. C. Beutler, A. E. Mark, R. C. van Schaik, P. R. Gerber, W. F. van Gunsteren, Chem. Phys. Letters 1994, 222, 529.
28. J. W. Pitera, W. F. van Gunsteren, Mol. Simul. 2002, 28, 45.
29. A. E. Mark, Y. Xu, H. Liu, W. F. van Gunsteren, Acta Biochim. Polonica 1995, 42, 525.
30. W. F. van Gunsteren, S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, A. E. Mark, W. R. P. Scott, I. G. Tironi, 'Biomolecular Simulation: The GROMOS96 Manual and User Guide', Vdf Hochschulverlag AG an der ETHZ, Zürich, 1996.
31. A. E. Mark, S. P. van Helden, P. E. Smith, L. H. M. Janssen, W. F. van Gunsteren, J. Am. Chem. Soc. 1994, 116, 6293.
32. X. Daura, P. H. Hünenberger, A. E. Mark, E. Querol, F. X. Avilés, W. F. van Gunsteren, J. Am. Chem. Soc. 1996, 118, 6285.
33. H. Schäfer, W. F. van Gunsteren, A. E. Mark, J. Comput. Chem. 1999, 20, 1604.
34. J. W. Pitera, W. F. van Gunsteren, J. Phys. Chem. B 2001, 105, 11264.
35. B. C. Oostenbrink, J. W. Pitera, M. M. H. van Lipzig, J. H. N. Meerman, W. F. van Gunsteren, J. Med. Chem. 2000, 43, 4594.
36. A. Villa, A. E. Mark, J. Comput. Chem., submitted.
37. R. Bürgi, F. Läng, W. F. van Gunsteren, Mol. Simul. 2001, 27, 215.
38. R. Zangi, H. Kovacs, W. F. van Gunsteren, J. Johansson, A. E. Mark, Proteins: Struct. Funct. Genet. 2001, 43, 395.
39. F. Fraternali, W. F. van Gunsteren, Biopolymers 1994, 34, 347.
40. T. C. Beutler, W. F. van Gunsteren, J. Chem. Phys. 1994, 100, 1492.
41. T. C. Beutler, W. F. van Gunsteren, J. Chem. Phys. Lett. 1995, 237, 308.
42. T. C. Beutler, T. Bremi, R. R. Ernst, W. F. van Gunsteren, J. Phys. Chem. 1996, 100, 2637.