Modeling chemical and biological systems: A successful course for undergraduate students

Journal of Chemical Education

Volumn 81, Issue 1, 2004, Pages 72-75

  Ramos, Maria João ^a   Fernandes, Pedro Alexandrino ^a   Melo, André ^a  

^a UNIVERSITY OF PORTO   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER PROGRAM LISTINGS; COMPUTER SIMULATION; CURRICULA; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; NUMERICAL ANALYSIS; QUANTUM THEORY; STUDENTS;

BIOLOGICAL SYSTEMS; CHEMICAL SYSTEMS; IONIC SALT; UNDERGRADUATE STUDENTS;

ENGINEERING EDUCATION;

EID: 0347603485     PISSN: 00219584     EISSN: None     Source Type: Journal    
DOI: 10.1021/ed081p72     Document Type: Article

References (19)

1. Fernandes, P. A.; Ramos, M. J. Notas em Mecânica Quântica e Dinâmica Molecular; Faculty of Sciences: University of Porto, 2001.
2. Magalhães, A. L. Sistema Operativo LINUX & Linguagem de Programação FORTRAN, Faculty of Sciences: University of Porto, 2000.
3. Feller, D.; Davidson, E. Basis Sets for Ab Initio Molecular Orbital Calculations and Intermolecular Interactions. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH Publishers, Inc.: New York, 1990; Vol. 1, p 1.
4. Stewart, J. J. P. Semiempirical Molecular Orbital Methods. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH Publishers, Inc.: New York, 1990; Vol. 1, p 45.
5. Lybrand, T. P. Computer Simulation of Biomolecular Systems Using Molecular Dynamics and Free Energy Perturbation Methods. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH Publishers, Inc.: New York, 1990; Vol. 1, p 295.
6. Boyd, D. B. Aspects of Molecular Modeling. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH Publishers, Inc.: New York, 1990; Vol. 1, p 321.
7. Bowen, J. P.; Allinger, N. L. Molecular Mechanics: The Art and Science of Parameterization. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH Publishers, Inc.: New York, 1990; Vol. 1, p 81.
8. Dinur, U.; Hagler, A. T. New Approaches to Empirical Force Fields. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH Publishers, Inc.: New York, 1990; Vol. 1, p 99.
9. McKee, M. L, Computing Reaction Pathways on Molecular Potential Energy Surfaces. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH Publishers, Inc.: New York, 1990; Vol. 1, p 35.
10. Pettersson, I.; Liljefors, T. Molecular Mechanics Calculated Conformational Energies of Organic Molecules: A Comparison of Force Fields. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH Publishers, Inc.: New York, 1990; Vol. 1, p 167.
11. Forrester, T.; Smith, W. DL_POLY (2.1 version); CCLRC: Daresbury Laboratory, Daresbury, United Kingdom, 1995.
12. Stewart, J. J. P. J. Comp. Chem. 1989, 10, 209.
13. Stewart, J. J. P. QCPE Program no. 455, 1983.
14. Schaftenaar, G.; Noordik, J. H. J. Comput-Aided Mol. Design 2000, 14, 123.
15. Gnuplot Central Home Page. http://www.gnuplot.info/ (accessed Oct 2003).
16. (a) Guex, N.; Peitsch, M. C. Electrophoresis 1997, 18, 2714.
17. (b) Deep View-Swiss PDB Viewer Home Page. http://us.expasy.org/spdbvl/mainpage.htm; http://us.expasy.org/spdbvl/text/getsgi.htm (both accessed Oct 2003).
18. Dewar, M. J. S.; Zoebisch, E. G.; Heale, F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 107.
19. Passarge, E. Color Atlas of Genetics, 2nd ed.; Thieme Medical Publishers, Inc.: New York, 2001.