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Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: Aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases
P. Cieplak, J. Caldwell, and P. Kollman Journal of Computational Chemistry 22(10):1048-1057 (2001)
to imported by lpk and 1 other user on Mar 1, 2008, 12:16 AM
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DETERMINING ATOM-CENTERED MONOPOLES FROM MOLECULAR ELECTROSTATIC POTENTIALS - THE NEED FOR HIGH SAMPLING DENSITY IN FORMAMIDE CONFORMATIONAL-ANALYSIS
C. M. Breneman, and K. B. Wiberg Journal of Computational Chemistry 11(3):361-373 (1990)
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Note on an Approximation Treatment for Many-Electron Systems
C. Moller, and M.S. Plesset Physical Review (1934)
to imported by lpk and 1 other user on Mar 1, 2008, 12:16 AM
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High performance computational chemistry: An overview of NWChem a distributed parallel application
R. A. Kendall, E. Apra, D. E. Bernholdt, E. J. Bylaska, M. Dupuis, G. I. Fann, R. J. Harrison, J. L. Ju, J. A. Nichols, J. Nieplocha, T. P. Straatsma, T. L. Windus, and A. T. Wong Computer Physics Communications 128(1-2):260-283 (2000)
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NWChem, A Computational Chemistry Package for Parallel Computers, Version 5.0, Pacific Northwest National Laboratory, Richland, Washington 99352-0999, USA
E. J. Bylaska, W. A. de Jong, K. Kowalski, T. P. Straatsma, M. Valievand D. Wang, E. Aprà, T. L. Windusand S. Hirata, M. T. Hackler, Y. Zhao, P.-D. Fan, R. J. Harrison, M. Dupuis, D. M. A. Smith, J. Nieplocha, V. Tipparaju, M. Krishnan, A. A. Auer, M. Nooijen, E. Brown, G. Cisnerosand, G. I. Fann, H. Früchtl, J. Garza, K. Hirao, R. Kendall, J. A. Nichols, K. Tsemekhman, K. Wolinski, J. Anchell, D. Bernholdt, P. Borowski, T. Clark, D. Clerc, H. Dachsel, M. Deegan, K. Dyall, D, Elwood, E. Glendening, M. Gutowski, A. Hess, J. Jaffe, B. Johnson, J. Ju, R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield, X. Longand B. Meng, T. Nakajima, S. Ni, L. Pollack, M. Rosing, G. Sandrone, M. Stave, H. Taylorand G. Thomas, J. van Lenthe, A. Wong, and Z. Zhang (2006)
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COMPACT EFFECTIVE POTENTIALS AND EFFICIENT SHARED-EXPONENT BASIS-SETS FOR THE 1ST-ROW AND 2ND-ROW ATOMS
W. J. Stevens, H. Basch, and M. Krauss Journal of Chemical Physics 81(12):6026-6033 (1984)
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A second generation force field for the simulation of proteins, nucleic acids, and organic molecules vol 117, pg 5179, 1995
W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman Journal of the American Chemical Society 118(9):2309-2309 (1996)
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Empirical force fields for biological macromolecules: Overview and issues
A. D. Mackerell Journal of Computational Chemistry 25(13):1584-1604 (2004)
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IMPORTANCE OF ATTRACTIVE VANDERWAALS CONTRIBUTION IN EMPIRICAL ENERGY FUNCTION MODELS FOR THE HEAT OF VAPORIZATION OF POLAR LIQUIDS
A. D. Mackerell, and M. Karplus Journal of Physical Chemistry 95(26):10559-10560 (1991)
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Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds
I. J. Chen, D. X. Yin, and A. D. MacKerell Journal of Computational Chemistry 23(2):199-213 (2002)
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A molecular mechanics force field for biologically important sterols
Z. Cournia, J. C. Smith, and G. M. Ullmann Journal of Computational Chemistry 26(13):1383-1399 (2005)
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Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching
A. C. Vaiana, A. Schulz, J. Wolfrum, M. Sauer, and J. C. Smith Journal of Computational Chemistry 24(5):632-639 (2003)
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Harmonic vibrational frequencies: An evaluation of Hartree-Fock, Moller-Plesset, quadratic configuration interaction, density functional theory, and semiempirical scale factors
A. P. Scott, and L. Radom Journal of Physical Chemistry 100(41):16502-16513 (1996)
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AFMM: A molecular mechanics force field vibrational parametrization program
A. C. Vaiana, Z. Cournia, I. B. Costescu, and J. C. Smith Computer Physics Communications 167(1):34-42 (2005)
to imported by lpk and 1 other user on Mar 1, 2008, 12:16 AM
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COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR SIMULATING LIQUID WATER
W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein Journal of Chemical Physics 79(2):926-935 (1983)
to imported by lpk and 1 other user on Mar 1, 2008, 12:16 AM
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All-atom empirical potential for molecular modeling and dynamics studies of proteins
A. D. MacKerell, D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus Journal of Physical Chemistry B 102(18):3586-3616 (1998)
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CHARMM - A PROGRAM FOR MACROMOLECULAR ENERGY, MINIMIZATION, AND DYNAMICS CALCULATIONS
B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus Journal of Computational Chemistry 4(2):187-217 (1983)
to imported by lpk and 3 other users on Mar 1, 2008, 12:16 AM
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Scalable molecular dynamics with NAMD
J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, and K. Schulten Journal of Computational Chemistry 26(16):1781-1802 (2005)
to imported by lpk and 1 other user on Mar 1, 2008, 12:16 AM
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Additive and classical drude polarizable force fields for linear and cyclic ethers
I. Vorobyov, V. M. Anisimov, S. Greene, R. M. Venable, A. Moser, R. W. Pastor, and A. D. MacKerell Journal of Chemical Theory and Computation 3(3):1120-1133 (2007)
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Swelling behavior of the cellulose I beta crystal models by molecular dynamics
T. Yui, S. Nishimura, S. Akiba, and S. Hayashi Carbohydrate Research 341(15):2521-2530 (2006)
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