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United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field.

Ulmschneider JP, Ulmschneider MB.

J Chem Theory Comput. 2009 Jul 14;5(7):1803-13. doi: 10.1021/ct900086b.


All-atom empirical potential for molecular modeling and dynamics studies of proteins.

MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FT, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, WiĆ³rkiewicz-Kuczera J, Yin D, Karplus M.

J Phys Chem B. 1998 Apr 30;102(18):3586-616. doi: 10.1021/jp973084f.


Interaction of salicylate and a terpenoid plant extract with model membranes: reconciling experiments and simulations.

Khandelia H, Witzke S, Mouritsen OG.

Biophys J. 2010 Dec 15;99(12):3887-94. doi: 10.1016/j.bpj.2010.11.009.


On the hydration of the phosphocholine headgroup in aqueous solution.

Foglia F, Lawrence MJ, Lorenz CD, McLain SE.

J Chem Phys. 2010 Oct 14;133(14):145103. doi: 10.1063/1.3488998.


CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses.

Raman EP, Guvench O, MacKerell AD Jr.

J Phys Chem B. 2010 Oct 14;114(40):12981-94. doi: 10.1021/jp105758h.


Comparing simulated and experimental translation and rotation constants: range of validity for viscosity scaling.

Venable RM, Hatcher E, Guvench O, Mackerell AD Jr, Pastor RW.

J Phys Chem B. 2010 Oct 7;114(39):12501-7. doi: 10.1021/jp105549s.


Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types.

Klauda JB, Venable RM, Freites JA, O'Connor JW, Tobias DJ, Mondragon-Ramirez C, Vorobyov I, MacKerell AD Jr, Pastor RW.

J Phys Chem B. 2010 Jun 17;114(23):7830-43. doi: 10.1021/jp101759q.


CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses.

Guvench O, Hatcher ER, Venable RM, Pastor RW, Mackerell AD.

J Chem Theory Comput. 2009 Aug 20;5(9):2353-2370.


CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose.

Hatcher E, Guvench O, Mackerell AD.

J Phys Chem B. 2009 Sep 17;113(37):12466-76. doi: 10.1021/jp905496e.


CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.

Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, Mackerell AD Jr.

J Comput Chem. 2010 Mar;31(4):671-90. doi: 10.1002/jcc.21367.


Comparison of the extended isotropic periodic sum and particle mesh Ewald methods for simulations of lipid bilayers and monolayers.

Venable RM, Chen LE, Pastor RW.

J Phys Chem B. 2009 Apr 30;113(17):5855-62. doi: 10.1021/jp900843x.


Many-body polarization effects and the membrane dipole potential.

Harder E, Mackerell AD Jr, Roux B.

J Am Chem Soc. 2009 Mar 4;131(8):2760-1. doi: 10.1021/ja806825g.


Using the isotropic periodic sum method to calculate long-range interactions of heterogeneous systems.

Wu X, Brooks BR.

J Chem Phys. 2008 Oct 21;129(15):154115. doi: 10.1063/1.2992601.


Additive empirical force field for hexopyranose monosaccharides.

Guvench O, Greene SN, Kamath G, Brady JW, Venable RM, Pastor RW, Mackerell AD Jr.

J Comput Chem. 2008 Nov 30;29(15):2543-64. doi: 10.1002/jcc.21004.


Size and shape of detergent micelles determined by small-angle X-ray scattering.

Lipfert J, Columbus L, Chu VB, Lesley SA, Doniach S.

J Phys Chem B. 2007 Nov 1;111(43):12427-38. Epub 2007 Oct 9.


Dynamical motions of lipids and a finite size effect in simulations of bilayers.

Klauda JB, Brooks BR, Pastor RW.

J Chem Phys. 2006 Oct 14;125(14):144710.


An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer.

Klauda JB, Brooks BR, MacKerell AD Jr, Venable RM, Pastor RW.

J Phys Chem B. 2005 Mar 24;109(11):5300-11.


Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew.

Horn HW, Swope WC, Pitera JW, Madura JD, Dick TJ, Hura GL, Head-Gordon T.

J Chem Phys. 2004 May 22;120(20):9665-78.


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