Tag forcefield [78 articles] Export

Recent papers classified by the tag forcefield.

	Free energy profiles of amino acid side chain analogs near water-vapor interface obtained via MD simulations [My Copy] Journal of Computational Chemistry, Vol. 31, No. 1. (2010), pp. 204-216. by Alexey K. Shaytan, Victor A. Ivanov, Konstantin V. Shaitan, Alexei R. Khokhlov posted to solvation pmf free-energy forcefield by agrossfield on 2009-11-24 13:57:39 as
	Force Field Parametrization through Fitting on Inflection Points in Isotherms [My Copy] Physical Review Letters, Vol. 93, No. 8. (Aug 2004), 088302. by D. Dubbeldam, S. Calero, T. J. H. Vlugt, et al.R. Krishna, T. L. M. Maesen, E. Beerdsen, B. Smit posted to zeolite forcefield adsorption by zhaidong on 2009-11-15 02:40:36 as
	Bend-twist-stretch model for coarse elastic network simulation of biomolecular motion [My Copy] The Journal of Chemical Physics, Vol. 131, No. 7. (2009), 074112. by Joseph N. Stember, Willy Wriggers posted to forcefield enm allostery by anuragsethi on 2009-10-27 17:13:11 as along with 2 people sobolevnrm agrossfield
	The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations. [My Copy] Journal of Physical Chemistry B, Vol. 111, No. 27. (1 July 2007), pp. 7812-7824. by Siewert J. Marrink, H. J. Risselada, Serge Yefimov, D. P. Tieleman, Alex H. Vries posted to forcefield coarse_grain by anuragsethi on 2009-10-25 03:00:52 as along with 7 people and 2 groups sunrise A_Coletta_Thesis Marine choonpeng softsimu dimka sunnytov Structural Biology Group TorVergata Molecular dynamics in MSU
	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 review forcefield dynamics coarse_grain by anuragsethi on 2009-10-17 14:15:45 as along with 4 people and 1 group loison jmccammon flbarroso sobolevnrm McCammon
	Application of the RESP Methodology in the Parametrization of Organic Solvents [My Copy] The Journal of Physical Chemistry B, Vol. 102, No. 41. (1 October 1998), pp. 8070-8079. by Thomas Fox, Peter A. Kollman posted to forcefield chloroform by mikaellund on 2009-10-08 10:35:47 as along with 1 person and 1 group A_Coletta_Thesis Structural Biology Group TorVergata
	Sorption of organic solvents on the surface of crystalline syndiotactic polystyrene studied by molecular dynamics simulation [My Copy] Journal of Molecular Structure, Vol. 739, No. 1-3. (04 April 2005), pp. 27-32. by Y. Tamai, M. Fukuda posted to forcefield chloroform by mikaellund on 2009-10-08 10:34:37 as
	Molecular dynamics simulation of liquid mixtures of acetonitrile and chloroform [My Copy] The Journal of Physical Chemistry, Vol. 94, No. 19. (1 September 1990), pp. 7378-7385. by H. Kovacs, J. Kowalewski, A. Laaksonen posted to forcefield chloroform by mikaellund on 2009-10-08 10:29:02 as
	A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6 [My Copy] Journal of Computational Chemistry, Vol. 25, No. 13. (2004), pp. 1656-1676. by Chris Oostenbrink, Alessandra Villa, Alan E. Mark, Wilfred F. Van Gunsteren posted to md forcefield by dsmueller on 2009-10-05 14:25:41 as along with 6 people loison peyamin rodrigofaccioli whitead tji ashaytan
	All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins [My Copy] The Journal of Physical Chemistry B, Vol. 102, No. 18. (1 April 1998), pp. 3586-3616. by A. D. MacKerell, D. Bashford, M. Bellott, et al.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 III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus posted to md forcefield by dsmueller on 2009-10-05 13:03:05 as along with 12 people jmparks rpetrenko jrperillaj Diego_Prada oceanwind dfgreen mkrishna timg dimka ttjoseph papatonyhill ssomani
	Toward High-Resolution de Novo Structure Prediction for Small Proteins [My Copy] Science, Vol. 309, No. 5742. (16 September 2005), pp. 1868-1871. by Philip Bradley, Kira M. S. Misura, David Baker posted to protein forcefield folding by paddydu on 2009-09-16 14:26:34 as along with 11 people and 4 groups ucbcjbm kgutwin BragilMassoud ana barry thaliana jwm vavi marcius gbart thamelry structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Atomistic modelling of BaTiO3 based on first-principles calculations [My Copy] Journal of Physics: Condensed Matter, Vol. 11, No. 48. (1999), pp. 9679-9690. by S. Tinte, M. G. Stachiotti, M. Sepliarsky, R. L. Migoni, C. O. Rodriguez posted to titanate simulation forcefield batio3 barium by paddydu on 2009-09-15 17:35:45 as
	Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data [My Copy] Biophysical Journal, Vol. 97, No. 3. (05 August 2009), pp. 853-856. by Lauren Wickstrom, Asim Okur, Carlos Simmerling posted to lysozyme forcefield by allmensch on 2009-09-04 14:07:57 as
	Long-timescale molecular dynamics simulations of protein structure and function. [My Copy] Current opinion in structural biology, Vol. 19, No. 2. (08 April 2009), pp. 120-127. by John L. Klepeis, Kresten Lindorff-Larsen, Ron O. Dror, David E. Shaw posted to lysozyme forcefield by allmensch on 2009-09-04 13:52:14 as along with 11 people and 1 group xdeupi agrossfield bmduggan r2s2 apaydin kiekyon Borelli idoerg sobolevnrm edws paulschlesinger baker-group
	Polarization effects in molecular mechanical force fields [My Copy] Journal of Physics: Condensed Matter, Vol. 21, No. 33. (2009), 333102. by Piotr Cieplak, Francois-Yves Dupradeau, Yong Duan, Junmei Wang posted to dynamics forcefield by anuragsethi on 2009-08-04 02:38:12 as along with 1 person and 1 group jmccammon McCammon
	Parametrization of a reactive force field for aluminum hydride [My Copy] The Journal of Chemical Physics, Vol. 131, No. 4. (2009), 044501. by J. G. O. Ojwang, Rutger A. van Santen, Gert J. Kramer, Adri C. T. van Duin, William A. Goddard, III posted to forcefield by yzlab on 2009-08-02 13:43:01 as along with 1 person OjwangJGO
	Potential energy function for apatites [My Copy] Phys. Chem. Chem. Phys., Vol. 5, No. 3. (2003), pp. 635-639. by Sven Hauptmann, Hagen Dufner, Jurgen Brickmann, Stefan M. Kast, R. Stephen Berry posted to apatite forcefield by paddydu on 2009-07-07 14:21:56 as
	Conformational preferences of substituted prolines in the collagen triple helix [My Copy] Biopolymers, Vol. 64, No. 2. (2002), pp. 63-71. by Sean D. Mooney, Peter A. Kollman, Teri E. Klein posted to amber forcefield by paddydu on 2009-06-26 13:30:48 as
	A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides [My Copy] Journal of Computational Chemistry, Vol. 26, No. 15. (2005), pp. 1612-1616. by Sanghyun Park, Randall J. Radmer, Teri E. Klein, Vijay S. Pande posted to amber forcefield by paddydu on 2009-06-26 10:37:44 as
	Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Dian Jiao, Jiajing Zhang, Robert E. Duke, Guohui Li, Michael J. Schnieders, Pengyu Ren posted to forcefield free-energy implicit-solvent ligand-binding by agrossfield on 2009-06-16 13:07:49 as along with 2 people and 1 group flbarroso sobolevnrm baker-group
	Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 3. (1 May 2007), pp. 961-975. by Scott A. Showalter, Rafael Bruschweiler posted to folding forcefield by allmensch on 2009-06-16 11:34:29 as along with 3 people bmduggan pablocarb loison
	A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation [My Copy] J. Phys. Chem. B, Vol. 112, No. 22. (10 May 2008), pp. 6878-6886. by M. Scott Shell, Ryan Ritterson, Ken A. Dill posted to forcefield ras usa by allmensch on 2009-06-15 11:58:08 as along with 2 people onufriev middledomain
	Pairwise energies for polypeptide coarse-grained models derived from atomic force fields [My Copy] The Journal of Chemical Physics, Vol. 130, No. 19. (2009), 195103. by Marcos R. Betancourt, Sheyore J. Omovie posted to coarse-grain forcefield by agrossfield on 2009-05-22 12:23:42 as
	Molecular Dynamics Study of the Solvation of Calcium Carbonate in Water [My Copy] The Journal of Physical Chemistry B, Vol. 111, No. 42. (1 October 2007), pp. 12219-12227. by Fabien Bruneval, Davide Donadio, Michele Parrinello posted to aragonite calcite calcium carbonate forcefield solvation water by paddydu on 2009-04-27 19:07:21 as along with 1 person pimpim
	Molecular Mechanical and Molecular Dynamic Simulations of Glycoproteins and Oligosaccharides. 1. GLYCAM_93 Parameter Development [My Copy] The Journal of Physical Chemistry, Vol. 99, No. 11. (1 March 1995), pp. 3832-3846. by Robert J. Woods, Raymond A. Dwek, Christopher J. Edge, Bert Fraser-Reid posted to forcefield glycam by paddydu on 2009-03-03 15:01:30 as
	Calculated bulk and surface properties of sulfates [My Copy] Faraday Disc., Vol. 95 (1993), pp. 273-280. by Neil L. Allan, Andrew L. Rohl, David H. Gay, Catlow, Roger J. Davey, William C. Mackrodt posted to forcefield by paddydu on 2009-03-03 10:27:30 as
	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 amber forcefield gaff by paddydu on 2009-03-03 10:19:48 as along with 10 people and 1 group rdf nigham lillekatt xdeupi gane5h kazemi megs easybakemuffin AndreaColetta pavanghatty LabCompMed
	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 alanine amber charmm comparison dipeptide forcefield gromos plot protein ramachandran by paddydu on 2009-02-25 17:22:05 as along with 3 people Diego_Prada flbarroso allmensch
	Atomistic Simulations of Corrosion Inhibitors Adsorbed on Calcite Surfaces I. Force field Parameters for Calcite [My Copy] The Journal of Physical Chemistry B, Vol. 105, No. 44. (1 November 2001), pp. 10746-10752. by Sungu Hwang, Mario Blanco, William A. Goddard posted to calcite forcefield by paddydu on 2009-02-24 16:37:13 as along with 2 people pimpim taenneken
	Practical tools for molecular modeling of complex carbohydrates and their interactions with proteins [My Copy] Molecular Engineering, Vol. 5, No. 1. (1 March 1995), pp. 271-300. by Serge Pérez, Christophe Meyer, Anne Imberty posted to carbohydrate forcefield glycoprotein pim polysaccharide tripos by paddydu on 2009-02-24 15:12:10 as
	The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin [My Copy] Journal of the American Chemical Society, Vol. 110, No. 6. (1 March 1988), pp. 1657-1666. by William L. Jorgensen, Julian Tirado-Rives posted to forcefield md by LamBras on 2008-12-20 17:23:28 as along with 2 people rabio dfgreen
	Partial atomic charges of amino acids in proteins [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 56, No. 1. (2004), pp. 102-109. by Annick Thomas, Alain Milon, Robert Brasseur posted to forcefield memprotxtal partial_charges by cmura to the group MuraLab on 2008-11-18 15:55:44 as along with 1 person apaydin
	Influence of cis double-bond parametrization on lipid membrane properties: How seemingly insignificant details in force-field change even qualitative trends [My Copy] The Journal of Chemical Physics, Vol. 129, No. 10. (2008) by Hector M. Seara, Tomasz Róg, Mikko Karttunen, Ramon Reigada, Ilpo Vattulainen posted to forcefield md membraneproteins by yzlab on 2008-10-19 02:56:31 as along with 2 people cjryan softsimu
	Calculation of absolute protein-ligand binding free energy from computer simulations. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 19. (10 May 2005), pp. 6825-6830. by H. J. Woo, B. Roux posted to forcefield free_energy md by LamBras on 2008-09-25 08:44:20 as along with 4 people flbarroso ibuch ttjoseph ashaytan
	Systematic Comparison of Empirical Forcefields for Molecular Dynamic Simulation of Insulin [My Copy] J. Phys. Chem. B (12 August 2008) by Nevena Todorova, Sue F. Legge, Herbert Treutlein, Irene Yarovsky posted to forcefield by agrossfield on 2008-08-29 15:20:29 as along with 1 person middledomain
	A novel high resolution Calpha--Calpha distance dependent force field based on a high quality decoy set. [My Copy] Proteins, Vol. 65, No. 3. (15 November 2006), pp. 726-741. by R. Rajgaria, S. R. McAllister, C. A. Floudas posted to forcefield by newton1234 on 2008-06-25 16:12:21 as
	A molecular dynamics study of polarizable water [My Copy] Molecular Physics, Vol. 68, No. 3. (1989), pp. 563-581. by Peter Ahlström, Anders Wallqvist, Sven Engström, Bo Jönsson posted to computing forcefield md by mikaellund on 2008-06-24 14:45:09 as
	Computer simulations of NaCl association in polarizable water [My Copy] J. Chem. Phys., Vol. 100, No. 5. (1994), pp. 3757-3766. by David E. Smith, Liem X. Dang posted to forcefield by mikaellund on 2008-06-11 07:44:07 as
	Computational Study of Ion Binding to the Liquid Interface of Water [My Copy] J. Phys. Chem. B, Vol. 106, No. 40. (10 October 2002), pp. 10388-10394. by L. X. Dang posted to computing forcefield by mikaellund on 2008-06-09 17:02:29 as
	Detailed Study of Potassium Solvation Using Molecular Dynamics Techniques [My Copy] J. Phys. Chem. B, Vol. 103, No. 22. (3 June 1999), pp. 4714-4720. by T. M. Chang, L. X. Dang posted to computing forcefield by mikaellund on 2008-06-09 17:01:25 as
	Development of a Physics-Based Force Field for the Scoring and Refinement of Protein Models [My Copy] Biophys. J. (4 January 2008), biophysj.107.121947. by Liliana Wroblewska, Anna Jagielska, Jeffrey Skolnick posted to forcefield by biehl on 2008-05-23 14:25:06 as along with 1 person paulschlesinger
	Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function [My Copy] Journal of Computational Chemistry, Vol. 19, No. 14. (6 January 1998), pp. 1639-1662. by Garrett M. Morris, David S. Goodsell, Robert S. Halliday, et al.Ruth Huey, William E. Hart, Richard K. Belew, Arthur J. Olson posted to docking forcefield by LamBras on 2008-04-25 14:10:21 as along with 23 people and 2 groups trishul nickolay npt11tpn jamalex joule lna Lombardo_7 karinaecomp oteri A_Coletta_Thesis arlam dgruiz nachtalp P2324548 yongzhao peprovy tovrstra papatonyhill schlauchi carlescorbi middledomain andreramme UVA_mag_res Chang group TSRI_MGL
	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
	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
	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 4 people and 1 group sunnytov dimka xdeupi viktor21614 LabCompMed
	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
	Force Field Validation Using Protein Side Chain Prediction [My Copy] J. Phys. Chem. B, Vol. 106, No. 44. (7 November 2002), pp. 11673-11680. by M. P. Jacobson, G. A. Kaminski, R. A. Friesner, C. S. Rapp posted to forcefield md sidechain by LamBras on 2008-03-22 16:09:35 as

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polarizable	28
md	16
cg	10
hb	10
interaction	9
ion	8
protein	7
simulations	7
solvation	7
water	7
energyfunctions	6
math	6
structure	5
amber	4
docking	4
lipid	4
carbohydrate	3
chloroform	3
computing	3
conformation	3
dynamics	3
fee	3
gromos	3
hydration	3
minimization	3
peptide	3
aminoacids	2
calcite	2
coarse_grain	2
coulomb_screen	2
crystal	2
dft	2
evb	2
folding	2
free-energy	2
internal_coordinates	2
ligands	2
lr	2
lysozyme	2
membrane	2
modelling	2
molecular	2
nano	2
pmf	2
qc	2
qmmm	2
reactive	2
vdw	2
water-vapor	2
abinitio	1
adsorption	1
alanine	1
allostery	1
apatite	1
aragonite	1
autodock	1
baseflip	1
carbonate	1
charmm	1
coarse-grain	1
comparison	1
cvff23	1
dipeptide	1
enm	1
free_energy	1
functional	1
gaff	1
glycam	1
glycoprotein	1
gpu	1
hbond	1
hexane	1
implicit-solvent	1
interface	1
ligand-binding	1
liquid-liquid	1
mechanics	1
membraneproteins	1
memprotxtal	1
nma	1
partial_charges	1
pim	1
plot	1
pointing	1
polysaccharide	1
pulldown	1
ramachandran	1
ras	1
review	1
salt	1
screening	1
shellmodel	1
sidechain	1
simulation	1
thesis	1
titanate	1
top	1
tripos	1
usa	1
zeolite	1

Tag forcefield [78 articles] Export

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