Tag force-fields [106 articles] Export

Recent papers classified by the tag force-fields.

	Simulation of activation free energies in molecular systems [My Copy] The Journal of Chemical Physics, Vol. 105, No. 5. (1996), pp. 1902-1921. by Eyal Neria, Stefan Fischer, Martin Karplus posted to transition_path problems_fel_dof force-fields dialanine alanine by Diego_Prada on 2009-11-23 16:30:50 as along with 1 person timg
	Multiscale simulation of soft matter systems - from the atomistic to the coarse-grained level and back [My Copy] Soft Matter In Soft Matter, Vol. 5, No. 22. (2009), pp. 4357-4366. by Christine Peter, Kurt Kremer posted to soft_matter multiscale_modeling modeling force-fields coarse_grain by flbarroso on 2009-11-03 18:03:01 as along with 4 people and 1 group loison jmccammon anuragsethi sobolevnrm McCammon
	A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules [My Copy] Journal of the American Chemical Society, Vol. 117, No. 19. (1 May 1995), pp. 5179-5197. by Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, et al.Ian R. Gould, Kenneth M. Merz, David M. Ferguson, David C. Spellmeyer, Thomas Fox, James W. Caldwell, Peter A. Kollman posted to resp force-fields by softsimu on 2009-10-03 18:28:43 as along with 6 people Lombardo_7 coomteng flbarroso kgutwin pavanghatty dfgreen
	Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides† [My Copy] The Journal of Physical Chemistry B, Vol. 105, No. 28. (1 July 2001), pp. 6474-6487. by George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, William L. Jorgensen posted to opls force-fields by softsimu on 2009-10-03 18:27:34 as along with 3 people sunnytov arifor LamBras
	Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 35. (1 September 2006), pp. 17616-17626. by Berk Hess, Nico F. A. van der Vegt posted to force-fields by softsimu on 2009-10-03 18:27:08 as along with 6 people and 1 group arnaucordomi krapnik flbarroso Diego_Prada Marine ashaytan Molecular dynamics in MSU
	CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations [My Copy] Journal of Computational Chemistry, Vol. 25, No. 1. (2004), pp. 1-16. by Sandeep Patel, Charles L. Brooks posted to md force-fields electrostatics by flbarroso on 2009-09-12 23:36:16 as along with 1 person tovrstra
	Empirical energy functions for energy minimization and dynamics of nucleic acids [My Copy] Journal of Computational Chemistry, Vol. 7, No. 5. (1986), pp. 591-616. by Lennart Nilsson, Martin Karplus posted to md force-fields by flbarroso on 2009-09-12 23:35:23 as
	<FONT SIZE='-2'>CHARMM</FONT>: A program for macromolecular energy, minimization, and dynamics calculations [My Copy] Journal of Computational Chemistry, Vol. 4, No. 2. (1983), pp. 187-217. by Bernard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson, David J. States, S. Swaminathan, Martin Karplus posted to molecular_dynamics_package md force-fields by flbarroso on 2009-09-12 23:32:11 as along with 17 people anallam ubcg08l nickolay newton1234 kgutwin r2s2 rpetrenko oceanwind RamuAnandakrishnan tovrstra dfgreen Lombardo_7 dgront mmuecke rabio saravan gisle
	The multiscale coarse-graining method. III. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation [My Copy] The Journal of Chemical Physics, Vol. 131, No. 3. (2009), 034102. by Avisek Das, Hans C. Andersen posted to force-fields fmm coarse-grain by tomweingarten on 2009-08-26 18:33:57 as along with 3 people sobolevnrm dlimmer agrossfield
	Determination method of the balance of the secondary-structure-forming tendencies of force fields [My Copy] Molecular Simulation (2009) by Yoshitake Sakae, Yuko Okamoto posted to protein_structure prediction force-fields by flbarroso on 2009-08-25 18:21:24 as
	Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77, No. 1. (2009), pp. 38-51. by Yelena A. Arnautova, Yury N. Vorobjev, Jorge A. Vila, Harold A. Scheraga posted to structure scoring protein-structure near-native jcc force-fields aug09 by klexa on 2009-08-11 17:40:54 as
	CHAMBER: Comprehensive support for CHARMM force fields within the AMBER software [My Copy] International Journal of Quantum Chemistry, Vol. 9999, No. 9999. (2009), NA. by Michael F. Crowley, Mark J. Williamson, Ross C. Walker posted to amber charmm force-fields by carlosjavierna on 2009-08-05 17:05:49 as
	Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine ldquodipeptidesrdquo (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 50, No. 3. (15 February 2003), pp. 451-463. by Hao Hu, Marcus Elstner, Jan Hermans posted to amino dialanine force-fields by Diego_Prada on 2009-07-26 16:12:40 as along with 3 people flbarroso paddydu allmensch
	A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions [My Copy] The Journal of Chemical Physics, Vol. 112, No. 20. (2000), pp. 8910-8922. by Michael W. Mahoney, William L. Jorgensen posted to force-fields mc modeling water by flbarroso on 2009-07-21 18:30:14 as along with 2 people Lombardo_7 loison
	Evaluation of carbohydrate molecular mechanical force fields by quantum mechanical calculations. [My Copy] Carbohydrate research, Vol. 339, No. 5. (2 April 2004), pp. 937-948. by L. Hemmingsen, D. E. Madsen, A. L. Esbensen, L. Olsen, S. B. Engelsen posted to force-fields by flbarroso on 2009-07-19 19:05:27 as
	Comparison of database potentials and molecular mechanics force fields. [My Copy] Current opinion in structural biology, Vol. 7, No. 2. (April 1997), pp. 194-199. by J. Moult posted to database force-fields by flbarroso on 2009-07-19 19:04:26 as
	Potential energy functions. [My Copy] Current opinion in structural biology, Vol. 5, No. 2. (April 1995), pp. 205-210. by T. A. Halgren posted to force-fields by flbarroso on 2009-07-19 19:03:59 as
	Derivation of class II force fields. VI. Carbohydrate compounds and anomeric effects. [My Copy] Biopolymers, Vol. 45, No. 6. (May 1998), pp. 435-468. by M. J. Hwang, X. Ni, M. Waldman, C. S. Ewig, A. T. Hagler posted to force-fields by flbarroso on 2009-07-19 19:02:22 as
	CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model [My Copy] Journal of Computational Chemistry, Vol. 25, No. 12. (September 2004), pp. 1504-1514. by Sandeep Patel, Alexander D. Mackerell, Charles L. Brooks posted to force-fields md polarizable protein by flbarroso on 2009-07-19 02:20:49 as along with 1 person tovrstra
	A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations [My Copy] Journal of Computational Chemistry, Vol. 24, No. 16. (December 2003), pp. 1999-2012. by Yong Duan, Chun Wu, Shibasish Chowdhury, et al.Mathew C. Lee, Guoming Xiong, Wei Zhang, Rong Yang, Piotr Cieplak, Ray Luo, Taisung Lee, James Caldwell, Junmei Wang, Peter Kollman posted to force-fields by flbarroso on 2009-07-19 02:12:07 as along with 6 people and 1 group Vadikus ashaytan Lombardo_7 A_Coletta_Thesis xdeupi schlauchi LabCompMed
	The Amber biomolecular simulation programs. [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1668-1688. by David A. Case, Thomas E. Cheatham, Tom Darden, et al.Holger Gohlke, Ray Luo, Kenneth M. Merz, Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods posted to force-fields md simulation by flbarroso on 2009-07-17 20:00:48 as along with 18 people and 3 groups krapnik csrocha nickolay mmuecke charris5 pavanghatty tahereh62 lna jwm ttjoseph xdeupi tovrstra bilab RamuAnandakrishnan IrinaMoreira adilson_mohr mikaellund gisle Radiation_Damage Stressosome LabCompMed
	A new force field (ECEPP-05) for peptides, proteins, and organic molecules. [My Copy] The journal of physical chemistry. B, Vol. 110, No. 10. (16 March 2006), pp. 5025-5044. by Y. A. Arnautova, A. Jagielska, H. A. Scheraga posted to force-fields peptide protein by flbarroso on 2009-07-17 19:58:08 as along with 1 person AndreaColetta
	Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. [My Copy] The journal of physical chemistry. B, Vol. 111, No. 9. (8 March 2007), pp. 2242-2254. by D. L. Mobley, E. Dumont, J. D. Chodera, K. A. Dill posted to force-fields free_energy solvation by flbarroso on 2009-07-17 19:56:59 as along with 3 people tovrstra ashaytan bentenin
	Automated conformational energy fitting for force-field development. [My Copy] Journal of molecular modeling, Vol. 14, No. 8. (August 2008), pp. 667-679. by O. Guvench, A. D. MacKerell posted to force-fields by flbarroso on 2009-07-17 19:54:30 as
	Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator. [My Copy] Journal of computational chemistry, Vol. 30, No. 12. (September 2009), pp. 1821-1838. by P. E. Lopes, G. Lamoureux, A. D. Mackerell posted to drude force-fields polarizable by flbarroso on 2009-07-17 19:54:09 as along with 1 person middledomain
	CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2 July 2009), NA. by K. Vanommeslaeghe, E. Hatcher, C. Acharya, et al.S. Kundu, S. Zhong, J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov, A. D. Mackerell posted to drug-design force-fields modeling by flbarroso on 2009-07-17 19:53:19 as
	Temperature and Pressure Dependence of the AMOEBA Water Model [My Copy] The Journal of Physical Chemistry B, Vol. 108, No. 35. (1 September 2004), pp. 13427-13437. by Pengyu Ren, Jay W. Ponder posted to force-fields polarizable water by flbarroso on 2009-07-16 19:44:39 as
	Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field [My Copy] Journal of the American Chemical Society, Vol. 125, No. 50. (1 December 2003), pp. 15671-15682. by Alan Grossfield, Pengyu Ren, Jay W. Ponder posted to force-fields polarizable solvation by flbarroso on 2009-07-16 19:42:42 as
	The missing term in effective pair potentials [My Copy] The Journal of Physical Chemistry, Vol. 91, No. 24. (1 November 1987), pp. 6269-6271. by H. J. C. Berendsen, J. R. Grigera, T. P. Straatsma posted to force-fields water by flbarroso on 2009-07-16 19:39:57 as along with 1 person Lombardo_7
	A Modified MSEVB Force Field for Protonated Water Clusters† [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 13. (2 April 2009), pp. 4111-4118. by R. Kumar, R. A. Christie, K. D. Jordan posted to force-fields pk water by flbarroso on 2009-07-16 19:27:12 as
	Incorporating intramolecular degrees of freedom in simulations of polarizable liquid water [My Copy] Chemical Physics, Vol. 148, No. 2-3. (1 December 1990), pp. 439-449. by A. Wallqvist posted to force-fields liquids modeling polarizable water by flbarroso on 2009-07-16 17:27:20 as
	Application of a universal force field to main group compounds [My Copy] Journal of the American Chemical Society, Vol. 114, No. 25. (1 December 1992), pp. 10046-10053. by C. J. Casewit, K. S. Colwell, A. K. Rappe posted to force-fields by flbarroso on 2009-07-15 04:26:36 as
	Application of a universal force field to organic molecules [My Copy] Journal of the American Chemical Society, Vol. 114, No. 25. (1 December 1992), pp. 10035-10046. by C. J. Casewit, K. S. Colwell, A. K. Rappe posted to force-fields by flbarroso on 2009-07-15 04:26:08 as
	UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations [My Copy] Journal of the American Chemical Society In Journal of the American Chemical Society, Vol. 114, No. 25. (1 December 1992), pp. 10024-10035. by A. K. Rappe, C. J. Casewit, K. S. Colwell, W. A. Goddard, W. M. Skiff posted to force-fields by flbarroso on 2009-07-15 04:23:53 as along with 2 people rdf egonw
	Stochastic approach to force field evaluations: conformational analysis of raloxifene, a potential new therapeutic agent for post-menopausal osteoporosis [My Copy] Journal of Molecular Structure: THEOCHEM, Vol. 368 (27 September 1996), pp. 7-15. by D. Boyd posted to force-fields by flbarroso on 2009-07-15 00:48:00 as
	Empirical force field methods and molecular mechanics [My Copy] In Computer-Aided Molecular Design (1996), pp. 124-170. by J. Doucet, J. Weber posted to force-fields by flbarroso on 2009-07-15 00:47:48 as
	Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 26. (2 July 2009), pp. 9004-9015. by Robert B. Best, Gerhard Hummer posted to coil force-field force-fields helix hummer molecular-dynamics polypeptides by carlosjavierna on 2009-07-13 06:02:42 as
	Molecular mechanics and molecular dynamics study on azurin using extensible and systematic force field (ESFF) [My Copy] Journal of Molecular Structure: THEOCHEM, Vol. 907, No. 1-3. (15 August 2009), pp. 1-8. by V. Rajapandian, Sundar S. Raman, V. Hakkim, R. Parthasarathi, V. Subramanian posted to force-field force-fields by carlosjavierna on 2009-07-07 03:43:52 as
	An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 999A. (2008), NA. by Paul C. Whitford, Jeffrey K. Noel, Shachi Gosavi, Alexander Schug, Kevin Y. Sanbonmatsu, José N. Onuchic posted to ca_chain_models folding force-fields by flbarroso on 2009-06-28 17:59:31 as along with 1 person middledomain
	Protein simulations combining an all-atom force field with a Go term [My Copy] Journal of Physics: Condensed Matter, Vol. 19, No. 28. (2007) by Jan H. Meinke, Ulrich H. E. Hansmann posted to effective-potentials force-fields by flbarroso on 2009-06-24 18:21:35 as along with 1 person choonpeng
	Improving an all-atom force field [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 76, No. 1. (2007), 012901. by Sandipan Mohanty, U. H. E. Hansmann posted to force-fields by flbarroso on 2009-06-24 18:20:42 as
	Potential energy functions for atomic-level simulations of water and organic and biomolecular systems [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 19. (10 May 2005), pp. 6665-6670. by William L. Jorgensen, Julian Tirado-Rives posted to force-fields protein water by flbarroso on 2009-06-19 02:58:09 as along with 3 people r2s2 krapnik choonpeng
	Accurate effective pair potentials for polymer solutions [My Copy] The Journal of Chemical Physics, Vol. 114, No. 9. (2001), pp. 4296-4311. by P. G. Bolhuis, A. A. Louis, J. P. Hansen, E. J. Meijer posted to force-fields polymer by flbarroso on 2009-06-19 02:49:09 as along with 3 people mc1975 marat kaz229
	How to build a better pair potential for water [My Copy] The Journal of Chemical Physics, Vol. 114, No. 15. (2001), pp. 6720-6733. by Bertrand Guillot, Yves Guissani posted to force-fields liquids water by flbarroso on 2009-06-19 02:47:35 as
	Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems [My Copy] Science, Vol. 321, No. 5890. (8 August 2008), pp. 798-800. by Michael L. Klein, Wataru Shinoda posted to force-fields md modeling protein by flbarroso on 2009-06-18 18:47:24 as along with 7 people cjryan abebe skumagai zwang pbartlett dgront middledomain
	Solving the equations of motion for mixed atomistic and coarse-grained systems [My Copy] Molecular Simulation, Vol. 35, No. 10. (2009), pp. 962-973. by Jong H. Park, Andreas Heyden posted to force-fields md modeling by flbarroso on 2009-06-18 11:55:39 as along with 1 person sobolevnrm
	CHARMM: The biomolecular simulation program [My Copy] Journal of Computational Chemistry, Vol. 30, No. 10. (30 July 2009), pp. 1545-1614. by B. R. Brooks, C. L. Brooks, A. D. Mackerell, et al.L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus posted to md force-fields by flbarroso on 2009-06-16 22:34:24 as along with 9 people and 1 group dgront rodrigofaccioli mmuecke medic0747 jrperillaj xavierprat saravan sobolevnrm dimka baker-group
	Optimized parameters for continuum solvation calculations with carbohydrates. [My Copy] The journal of physical chemistry. B, Vol. 112, No. 16. (24 April 2008), pp. 5238-5249. by D. F. Green posted to continnum force-fields solvation by flbarroso on 2009-06-15 16:10:47 as along with 2 people and 1 group dfgreen sobolevnrm baker-group
	Water-like structure with repulsive double-core interactions [My Copy] Molecular Physics: An International Journal at the Interface Between Chemistry and Physics, Vol. 107, No. 13. (2009), pp. 1349-1353. by Aurélien Perera, Arnaud Rispe, Larisa Zorani&cacute;, Redha Mazighi, Franjo Sokoli&cacute; posted to force-fields water by flbarroso on 2009-06-15 13:28:36 as
	Dynamical fluctuating charge force fields: Application to liquid water [My Copy] The Journal of Chemical Physics, Vol. 101, No. 7. (1994), pp. 6141-6156. by Steven W. Rick, Steven J. Stuart, B. J. Berne posted to force-fields polarizable water by flbarroso on 2009-06-01 14:26:15 as along with 1 person tovrstra

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water	17
md	15
polarizable	12
modeling	7
protein	7
solvation	7
liquids	5
electrostatics	4
hexapeptide	4
dialanine	3
simulation	3
soft_matter	3
2009	2
aug09	2
experimental	2
folding	2
force-field	2
generalized-born	2
ions	2
jcc	2
molecular-dynamics	2
molecular_dynamics	2
multiscale	2
multiscale_modeling	2
near-native	2
opls	2
peptide	2
polarizability	2
polymer	2
protein-structure	2
scoring	2
short-peptides	2
structure	2
alanine	1
amber	1
amino	1
beta-hairpin	1
bias	1
ca_chain_models	1
calcium	1
carbohydrate	1
chapt_cmn	1
charges	1
charmm	1
coarse-grain	1
coarse-grained	1
coarse_grain	1
coil	1
continnum	1
database	1
dna	1
drude	1
drug-design	1
dynamics	1
effective-potentials	1
enzyme	1
ff	1
fluid	1
fmm	1
free_energy	1
helix	1
hummer	1
hydrophobicity	1
interactions	1
isomerization	1
lipids	1
magnesium	1
mc	1
membranes	1
micelles	1
molecular	1
molecular_dynamics_package	1
monte-carlo	1
peg	1
peptides	1
pk	1
pna	1
polypeptides	1
prediction	1
problems_fel_dof	1
protein-protein	1
protein_structure	1
proteins	1
qmmm	1
reaction-field	1
resp	1
rna	1
software	1
tip4p	1
transition_path	1

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