The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations

Journal of Physical Chemistry B - Tập 111 Số 27 - Trang 7812-7824 - 2007
‪Siewert J. Marrink1, Herre Jelger Risselada1, S. Yefimov1, D. Peter Tieleman1, Alex H. de Vries1
1Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, Zernike Institute for Advanced Materials, Department of Applied Physics, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands, and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary AB T2N 1N4, Canada

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Smit B., 1990, Nature, 348, 625, 10.1038/348624a0

Shillcock, J. C.; Lipowsky, R.J. Phys.  Condens.Matter2006,18, S1191−S1219.

Venturoli M., 2006, Phys. Lett., 437, 54

Müller M., 2006, Phys. Lett., 434, 176

Noguchi H., 2001, Phys. Rev. E, 64, 41913, 10.1103/PhysRevE.64.041913

Farago O., 2003, J. Chem. Phys., 119, 605, 10.1063/1.1578612

Müller M., 2003, Biophys. J., 85, 1623

Brannigan G., 2004, J. Chem. Phys., 120, 1071, 10.1063/1.1625913

Murtola T., 2004, J. Chem. Phys., 121, 9165, 10.1063/1.1803537

Sevink G. J. A., 2005, Macromolecules, 38, 7502, 10.1021/ma0506740

Cooke I. R., 2005, Phys. Rev. E, 72, 011506, 10.1103/PhysRevE.72.011506

Wang Z., 2005, J. Chem. Phys., 122, 234711, 10.1063/1.1927509

Goetz R., 1998, J. Chem. Phys., 108, 7409, 10.1063/1.476160

Venturoli M., 1999, Phys. Chem. Commun., 10, 5

Groot R. D., 2001, Biophys. J., 81, 736, 10.1016/S0006-3495(01)75737-2

Shillcock J. C., 2002, J. Chem. Phys., 117, 5061, 10.1063/1.1498463

den Otter W. K., 2003, J. Chem. Phys., 118, 4720, 10.1063/1.1543941

Stevens M. J., 2004, J. Chem. Phys., 121, 11948, 10.1063/1.1814058

Frink L. J. D., 2005, Phys. Rev. E, 72, 041923, 10.1103/PhysRevE.72.041923

Markvoort A. J., 2005, J. Phys. Chem. B, 109, 22654, 10.1021/jp053038c

Pool R., 2006, Phys. Chem. Chem. Phys., 8, 948, 10.1039/B512960E

Shelley J. C., 2001, J. Phys. Chem. B, 105, 4470, 10.1021/jp001672e

Marrink S. J., 2004, J. Phys. Chem. B, 108, 760, 10.1021/jp036508g

Izvekov S., 2005, J. Phys. Chem. B, 109, 2473

Lyubartsev A. P., 2005, Eur. Biophys. J. Biophys. Lett., 35, 61, 10.1007/s00249-005-0005-y

Elezgaray J., 2006, Comput. Phys. Commun., 175, 268, 10.1016/j.cpc.2006.01.009

Oostenbrink C., 2004, J. Comput. Chem., 25, 1676, 10.1002/jcc.20090

McWhirter J. L. L., 2004, Biophys. J., 87, 3263

Neri, M.; Anselmi, C.; Carnevale, V.; Vargiu, A. V.; Carloni, P.J. Phys. Condens.Matter2006,18, S347−S355.

Christen M., 2006, J. Chem. Phys., 124, 154106, 10.1063/1.2187488

Praprotnik M., 2005, J. Chem. Phys., 123, 224106, 10.1063/1.2132286

Marrink S. J., 2003, J. Am. Chem. Soc., 125, 15242

Marrink S. J., 2003, J. Am. Chem. Soc., 125, 11145

Kasson P. M., 2006, Proc. Natl. Acad. Sci. U.S.A., 103, 11921, 10.1073/pnas.0601597103

Marrink S. J., 2004, Biophys. J., 87, 3900, 10.1529/biophysj.104.048710

Faller R., 2004, J. Langmuir, 20, 7693, 10.1021/la0492759

Marrink S. J., 2005, Chem. Phys. Lipids, 135, 244, 10.1016/j.chemphyslip.2005.03.001

Bond P. J., 2006, J. Am. Chem. Soc., 128, 2704

Shih A. Y., 2006, J. Phys. Chem. B, 110, 3684

de Joannis J., 2006, Langmuir, 22, 1005, 10.1021/la051278d

Adhangale P. S., 2006, Mol. Phys., 104, 3019, 10.1080/00268970600935101

Baoukina S., J. Am. Chem. Soc.

Dickey A. N., 2005, J. Polym. Sci., 43, 1032, 10.1002/polb.20392

Notman M., 2006, J. Am. Chem. Soc., 128, 13983, 10.1021/ja063363t

Lee H., 2006, J. Phys. Chem. B, 110, 18211

Baron R., 2006, J. Phys. Chem. B, 110, 8473

Baron R., 2006, J. Phys. Chem. B, 110, 15614

Baron R., 2007, Chem. Phys. Chem., 8, 461

Humphrey W., 1996, J. Mol. Graphics, 14, 38, 10.1016/0263-7855(96)00018-5

Lindahl E., 2001, J. Mol. Model., 7, 317, 10.1007/s008940100045

van der Spoel D., 2005, J. Comput. Chem., 26, 1718, 10.1002/jcc.20291

Sonne J., 2005, J. Chem. Phys., 122, 124903, 10.1063/1.1862624

Oversteegen S. M., 2000, Phys. Rev. E, 62, 8461, 10.1103/PhysRevE.62.8453

Lindahl E., 2000, J. Chem. Phys., 113, 3893, 10.1063/1.1287423

Anézo C., 2003, J. Phys. Chem. B, 107, 9433, 10.1021/jp0348981

Gullingsrud J., 2005, Biophys. J., 86, 3509

Patra M., 2005, Eur. Biophys. J. Biophys. Lett., 35, 88, 10.1007/s00249-005-0011-0

Shkulipa, S. Computer Simulations of Lipid Bilayer Dynamics. Ph.D. thesis, University of Twente, The Netherlands, 2006.

Petrache H. I., 1998, Phys. Rev. E, 57, 7024, 10.1103/PhysRevE.57.7014

Lee C. H., 2001, Phys. Rev. E, 64, 020901, 10.1103/PhysRevE.64.020901

Shearman, G. C.; Ces, O.; Templer, R. H.; Seddon, J. M.J. Phys. Condens. Matter2006,18, S1105−S1124.

Rawicz W., 2000, Biophys. J., 79, 339, 10.1016/S0006-3495(00)76295-3

Tausk R. J. M., 1974, Biophys. Chem., 2, 63

Tieleman D. P., 2006, J. Am. Chem. Soc., 128, 12467, 10.1021/ja0624321

Torrie G. M., 1977, J. Comput. Phys., 23, 199, 10.1016/0021-9991(77)90121-8

Kumar S., 1992, J. Comput. Chem., 13, 1021, 10.1002/jcc.540130812

Israelachvili J. N., 1992, Intermolecular and surface forces

Schwarzenbach R. P., 2003, Enviromental Organic Chemistry

Karlsson R., 1973, J. Chem. Eng. Data, 18, 292, 10.1021/je60058a006

Lide D. R., 1992, CRC Handbook of Chemistry and Physics, 72 ed

McMullen T. P. W., 2004, Curr. Opin. Colloid Interface Sci., 8, 468

Smondyrev A., 1999, Biophys. J., 77, 2089, 10.1016/S0006-3495(99)77049-9

Chiu S. W., 2002, Biophys. J., 83, 1853

Hofsäss C., 2003, Biophys. J., 84, 2206, 10.1016/S0006-3495(03)75025-5

Edholm O., 2005, Biophys. J., 89, 1832, 10.1529/biophysj.105.064329

Duffy E. M., 2000, J. Am. Chem. Soc., 122, 2888, 10.1021/ja993663t

Cabani P., 1981, J. Solution Chem., 10, 595, 10.1007/BF00646936

Wolfenden R., 1981, Biochemistry, 20, 855, 10.1021/bi00507a030

Ruelle P., 1999, Chemosphere, 40, 512

Dolney D. M., 2000, J. Comput. Chem., 21, 366, 10.1002/(SICI)1096-987X(20000415)21:5<340::AID-JCC2>3.0.CO;2-M

Li J., 1999, Theor. Chim. Acta, 103, 63

Abraham M. H., 1990, J. Chem. Soc., Perkin Trans., 2, 300

Viswanadhan V. N., 1999, J. Chem. Inf. Comput. Sci., 39, 412, 10.1021/ci980154m

Hansch C., 1995, Exploring QSAR - Hydrophobic, Electronic, and Steric Constants

Amaya J., 2002, J. Solution Chem., 31, 148, 10.1023/A:1015201119955

Hamai C., 2006, Biophys. J., 90, 1248, 10.1529/biophysj.105.069435

Zimmerberg J., 2006, Nat. Rev. Mol. Cell Biol., 7, 19, 10.1038/nrm1784