easybakemuffin's library 34 articles Export

	Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with dioeerent macroscopic boundary conditions and parameters [My Copy] (1996) by E. Tieleman, D. Berendsen posted to lipid by easybakemuffin on 2008-06-11 15:22:26 as
	Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins [My Copy] Journal of Computational Chemistry, Vol. 16, No. 11. (1995), pp. 1357-1377. by Piotr Cieplak, Wendy D. Cornell, Christopher Bayly, Peter A. Kollman posted to forcefield by easybakemuffin on 2008-04-10 18:27:38 as along with 3 people Lombardo_7 RamuAnandakrishnan AndreaColetta
	Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. [My Copy] Biophysical journal, Vol. 79, No. 1. (1 July 2000), pp. 426-433. by E. Lindahl, O. Edholm posted to membrane by easybakemuffin on 2008-04-10 17:26:04 as along with 2 people and 1 group sunnytov sobolevnrm baker-group
	Molecular Simulation Study of Structural and Dynamic Properties of Mixed DPPC/DPPE Bilayers. [My Copy] Biophys J (13 March 2006) by Sukit Leekumjorn, Amadeu K K. Sum posted to membrane by easybakemuffin on 2008-04-10 14:40:17 as along with 4 people sunhwan dimka yoel_rf softsimu
	Molecular dynamics simulation of a palmitoyl-oleoyl phosphatidylserine bilayer with Na+ counterions and NaCl. [My Copy] Biophys J, Vol. 86, No. 3. (March 2004), pp. 1601-1609. by P. Mukhopadhyay, L. Monticelli, D. P. Tieleman posted to membrane by easybakemuffin on 2008-04-10 14:37:16 as along with 3 people dimka softsimu robertvacha
	Molecular Dynamics Simulations of Ternary Membrane Mixture: Phosphatidylcholine, Phosphatidic Acid, and Cholesterol. [My Copy] J Phys Chem B (5 December 2007) by Mary H. Cheng, Lu T. Liu, Alexander C. Saladino, Yan Xu, Pei Tang posted to membrane by easybakemuffin on 2008-04-10 14:31:20 as along with 2 people and 1 group dimka sobolevnrm baker-group
	Development and testing of a general amber force field. [My Copy] J Comput Chem, Vol. 25, No. 9. (15 July 2004), pp. 1157-1174. by J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, D. A. Case posted to forcefield by easybakemuffin on 2008-04-08 15:02:51 as along with 10 people and 1 group rdf paddydu nigham lillekatt xdeupi gane5h kazemi megs AndreaColetta pavanghatty LabCompMed
	Structure and dynamics of phospholipid bilayers using recently developed general all-atom force fields [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2007), NA. by Lula Rosso, Ian R. Gould posted to forcefield lipid by easybakemuffin on 2008-04-08 15:00:51 as along with 2 people and 1 group daevans sobolevnrm baker-group
	Parametrization of aliphatic CH$_n$ united atoms of GROMOS96 force field [My Copy] Journal of Computational Chemistry, Vol. 19, No. 5. (1998), pp. 535-547. by Xavier Daura, Alan E. Mark, Wilfred F. Van Gunsteren posted to forcefield membrane by easybakemuffin on 2008-04-08 14:04:36 as along with 2 people peyamin marceavi
	Optimization of Hydrocarbon Chain Interaction Parameters: Application to the Simulation of Fluid Phase Lipid Bilayers [My Copy] J Phys Chem B, Vol. 103 (1999), pp. 6323-7. by S. W. Chiu, M. M. Clark, Eric Jakobsson, Shankar Subramaniam, Larry H. Scott posted to forcefield membrane by easybakemuffin on 2008-04-08 14:00:37 as along with 1 person isarfox
	How lipids affect the activities of integral membrane proteins. [My Copy] Biochim Biophys Acta, Vol. 1666, No. 1-2. (3 November 2004), pp. 62-87. by A. G. Lee posted to membrane-bound protein by easybakemuffin on 2008-04-08 13:42:04 as
	Computer simulation of membrane proteins [My Copy] Biochim. Biophys. Acta, Vol. 1666, No. 1--2. (November 2004), pp. 158-189. by Walter L. Ash, Marian R. Zlomislic, Eliud O. Oloo, Peter D. Tieleman posted to membrane-bound protein by easybakemuffin on 2008-04-08 13:36:37 as along with 1 person softsimu
	The Lateral Pressure Profile in Membranes: A Physical Mechanism of General Anesthesia [My Copy] Biochemistry, Vol. 36, No. 9. (4 March 1997), pp. 2339-2344. by R. S. Cantor posted to membrane-bound protein by easybakemuffin on 2008-04-07 15:53:29 as
	Lipids do influence protein function---the hydrophobic matching hypothesis revisited [My Copy] Biochim. Biohys. Acta. Biomembr., Vol. 1666 (November 2004), pp. 205-226. by M. O. Jensen, O. G. Mouritsen posted to membrane-bound protein by easybakemuffin on 2008-04-07 15:33:54 as along with 1 person softsimu
	Performance of the general amber force field in modeling aqueous POPC membrane bilayers [My Copy] Journal of Computational Chemistry, Vol. 28, No. 12. (12 April 2007), pp. 2051-2058. by Balázs Jójárt, Tamás A. Martinek posted to forcefield membrane by easybakemuffin on 2008-04-06 15:34:42 as along with 3 people and 1 group dimka xdeupi viktor21614 LabCompMed
	A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. [My Copy] Biochim Biophys Acta, Vol. 1331, No. 3. (21 November 1997), pp. 235-270. by D. P. Tieleman, S. J. Marrink, H. J. Berendsen posted to membrane by easybakemuffin on 2008-04-03 23:53:31 as along with 1 person davidng
	A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems [My Copy] (1997) by D. Tieleman, S. Marrink, H. Berendsen posted to membrane by easybakemuffin on 2008-04-03 23:49:52 as
	Constant surface tension simulations of lipid bilayers: The sensitivity of surface areas and compressibilities [My Copy] J. Chem. Phys., Vol. 111, No. 3. (July 1999), pp. 1281-1287. by Scott E. Feller, Richard W. Pastor posted to membrane by easybakemuffin on 2008-03-31 15:48:57 as along with 1 person softsimu
	Constant pressure molecular dynamics algorithms [My Copy] The Journal of Chemical Physics, Vol. 101, No. 5. (1994), pp. 4177-4189. by Glenn J. Martyna, Douglas J. Tobias, Michael L. Klein posted to nose-hoover pressure by easybakemuffin on 2008-03-26 18:17:53 as along with 2 people dimka rpetrenko
	Constant pressure molecular dynamics simulation: The Langevin piston method [My Copy] The Journal of Chemical Physics, Vol. 103, No. 11. (1995), pp. 4613-4621. by Scott E. Feller, Yuhong Zhang, Richard W. Pastor, Bernard R. Brooks posted to langevin pressure by easybakemuffin on 2008-03-26 18:08:10 as along with 2 people dimka rpetrenko
	An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids [My Copy] J. Phys. Chem. B, Vol. 104, No. 31. (10 August 2000), pp. 7510-7515. by S. E. Feller, Jr Mackerell posted to forcefield lipid by easybakemuffin on 2008-03-26 17:54:59 as along with 1 person and 1 group Marine Molecular dynamics in MSU
	All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data [My Copy] Journal of Computational Chemistry, Vol. 21, No. 2. (2000), pp. 86-104. by Nicolas Foloppe, Alexander D. Mackerell, Jr posted to forcefield lipid by easybakemuffin on 2008-03-26 17:47:14 as along with 3 people dimka rpetrenko mkrishna
	An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer [My Copy] J. Phys. Chem. B, Vol. 109, No. 11. (24 March 2005), pp. 5300-5311. by J. B. Klauda, B. R. Brooks, A. D. Mackerell, R. M. Venable, R. W. Pastor posted to forcefield lipid by easybakemuffin on 2008-03-26 17:44:33 as along with 1 person dimka
	Particle mesh Ewald: An N [center-dot] log(N) method for Ewald sums in large systems [My Copy] The Journal of Chemical Physics, Vol. 98, No. 12. (1993), pp. 10089-10092. by Tom Darden, Darrin York, Lee Pedersen posted to pme by easybakemuffin on 2008-03-26 17:03:57 as along with 12 people sunnytov bmduggan rpetrenko r2s2 robertvacha A_Coletta_Thesis mleis and_ped10 allmensch RamuAnandakrishnan tji ashaytan
	A smooth particle mesh Ewald method [My Copy] The Journal of Chemical Physics, Vol. 103, No. 19. (1995), pp. 8577-8593. by Ulrich Essmann, Lalith Perera, Max L. Berkowitz, Tom Darden, Hsing Lee, Lee G. Pedersen posted to pme by easybakemuffin on 2008-03-26 17:03:41 as along with 15 people and 2 groups jmparks rpetrenko A_Coletta_Thesis r2s2 charris5 pavanghatty sobolevnrm choonpeng lillekatt and_ped10 RamuAnandakrishnan ashaytan mikaellund 6rheology jteyra Structural Biology Group TorVergata baker-group
	Comparison of simple potential functions for simulating liquid water [My Copy] The Journal of Chemical Physics, Vol. 79, No. 2. (1983), pp. 926-935. by William L. Jorgensen, Jayaraman Chandrasekhar, Jeffry D. Madura, Roger W. Impey, Michael L. Klein posted to tip3p by easybakemuffin on 2008-03-26 17:03:19 as along with 17 people and 1 group jmparks fralium bmduggan kulinskii ibuch Lombardo_7 paddydu dfgreen softsimu mleis ttjoseph ffranca ashaytan RamuAnandakrishnan r2s2 pavanghatty Diego_Prada CMB
	Packing and Viscoelasticity of Polyunsaturated $ω$-3 and $ω$-6 Lipid Bilayers as Seen by $^2$H NMR and X-ray Diffraction [My Copy] Journal of the American Chemical Society, Vol. 127, No. 5. (2005), pp. 1576-1588. by K. Rajamoorthi, H. I. Petrache, T. J. Mcintosh, M. F. Brown posted to membrane by easybakemuffin on 2007-06-06 16:14:41 as
	Structure of Fully Hydrated Fluid Phase Lipid Bilayers with Monounsaturated Chains. [My Copy] Journal of Membrane Biology, Vol. 208, No. 3. (2006), pp. 193-202. by N. Kucerka, Tristram S. Nagle, J. F. Nagle posted to bibtex-import by easybakemuffin on 2007-06-06 15:43:00 as
	Lipid Bilayers Driven to a Wrong Lane in Molecular Dynamics Simulations by Subtle Changes in Long-Range Electrostatic Interactions [My Copy] Journal of Physical Chemistry B, Vol. 108, No. 14. (2004), pp. 4485-4494. by M. Patra, M. Karttunen, M. T. Hyvonen, E. Falck, I. Vattulainen posted to bibtex-import by easybakemuffin on 2007-06-06 14:41:59 as
	Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions. [My Copy] Biophys J, Vol. 84, No. 6. (June 2003), pp. 3636-3645. by M. Patra, M. Karttunen, M. T. Hyvönen, E. Falck, P. Lindqvist, I. Vattulainen posted to membrane by easybakemuffin on 2007-06-06 14:40:17 as along with 2 people dimka softsimu
	Molecular dynamics simulations of gramicidin A in a lipid bilayer: From structure-function relations to force fields [My Copy] Chemistry and Physics of Lipids In Protein:Lipid Interactions - COST action D22 meeting, Vol. 141, No. 1-2. (June 2006), pp. 197-204. by Turgut Bastug, Swarna M. Patra, Serdar Kuyucak posted to membrane by easybakemuffin on 2007-06-06 14:38:53 as along with 1 person somoney
	Polyunsaturation in Lipid Membranes: Dynamic Properties and Later Pressure Profiles [My Copy] Journal of Physical Chemistry B, Vol. 111, No. 12. (2007), pp. 3139-3150. by Samuli Ollila, Marja T. Hyv$ö$nen, Ilpo Vattulainen posted to membrane by easybakemuffin on 2007-06-06 14:37:05 as
	Free Volume Properties of Sphingomyelin, DMPC, DPPC, and PLPC Bilayers [My Copy] Journal of Computational and Theoretical Nanoscience, Vol. 2, No. 3. (September 2005), pp. 401-413. by M. Kupiainen, E. Falck, S. Ollila, et al.P. Niemela, A. A. Gurtovenko, M. T. Hyvonen, M. Patra, M. Karttunen, I. Vattulainen posted to membrane by easybakemuffin on 2007-06-06 14:35:50 as
	Computer Simulation of a DPPC Phospholipid Bilayer: Structural Changes as a Function of Molecular Surface Area [My Copy] Langmuir, Vol. 13, No. 24. (1997), pp. 6555-6561. by S. E. Feller, R. M. Venable, R. W. Pastor posted to membrane by easybakemuffin on 2007-06-06 14:29:42 as