Tag charmm [47 articles] Export

Recent papers classified by the tag charmm.

	CHARMM: A program for macromolecular energy, minimization, and dynamics calculations [My Copy] Journal of Computational Chemistry, Vol. 4, No. 2. (FebruaryFebruary 1983), pp. 187-217. by Bernard .. Brooks,, Robert .. Bruccoleri,, Barry .. Olafson,, David .. States,, S. Swaminathan,, Martin Karplus, posted to charmm by ckmyo on 2009-12-15 09:03:49 as along with 18 people anallam ubcg08l flbarroso nickolay newton1234 kgutwin r2s2 rpetrenko oceanwind RamuAnandakrishnan tovrstra dfgreen Lombardo_7 dgront mmuecke rabio saravan gisle
	Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme. [My Copy] Biophys J, Vol. 90, No. 4. (15 February 2006) by M. Buck, S. Bouguet-Bonnet, R. W. Pastor, A. D. MacKerell posted to molecular_dynamics charmm by jmparks on 2009-10-15 16:43:58 as along with 1 person allmensch
	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, 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, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus posted to molecular_dynamics force_field charmm by jmparks on 2009-10-15 16:39:07 as along with 12 people dsmueller rpetrenko jrperillaj Diego_Prada oceanwind dfgreen mkrishna timg dimka ttjoseph papatonyhill ssomani
	CHARMM Additive All-Atom Force Field for Aldopentofuranoses, Methyl-aldopentofuranosides, and Fructofuranose [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Elizabeth Hatcher, Olgun Guvench, Alexander D. Mackerell posted to nmr force field development charmm by whitead to the group Jiang Research Group on 2009-08-25 17:12:03 as
	How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines [My Copy] The Journal of Chemical Physics, Vol. 109, No. 18. (1998), pp. 7678-7693. by Markus Deserno, Christian Holm posted to molecular_dynamics charmm by mmuecke on 2009-08-14 08:41:40 as along with 1 person stephenbond
	How to mesh up Ewald sums. II. An accurate error estimate for the particle--particle--particle-mesh algorithm [My Copy] The Journal of Chemical Physics, Vol. 109, No. 18. (1998), pp. 7694-7701. by Markus Deserno, Christian Holm posted to molecular_dynamics error_analysis charmm by mmuecke on 2009-08-14 08:38:56 as along with 1 person stephenbond
	The Amber biomolecular simulation programs. [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1668-1688. by D. A. Case, T. E. Cheatham, T. Darden, et al.H. Gohlke, R. Luo, K. M. Merz, A. Onufriev, C. Simmerling, B. Wang, R. J. Woods posted to charmm molecular_dynamics by mmuecke on 2009-08-11 11:19:47 as along with 18 people and 3 groups krapnik csrocha nickolay flbarroso charris5 pavanghatty tahereh62 lna jwm ttjoseph xdeupi tovrstra bilab RamuAnandakrishnan IrinaMoreira adilson_mohr mikaellund gisle Radiation_Damage Stressosome LabCompMed
	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
	Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension [My Copy] Biophysical Journal, Vol. 92, No. 12. (15 June 2007), pp. 4157-4167. by J. Sonne, M. Jensen, F. Hansen, L. Hemmingsen, G. Peters posted to charmm lipids md parameterization by dimka on 2009-07-27 20:29:25 as along with 1 person arnaucordomi
	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 charmm charmm27 force-field lipid md by dimka on 2009-07-27 20:26:34 as along with 3 people rpetrenko mkrishna easybakemuffin
	ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 6. (9 June 2009), pp. 1632-1639. by M. J. Harvey, G. Giupponi, G. De Fabritiis posted to charmm gpu molecular_dynamics by mmuecke on 2009-06-30 16:22:21 as along with 4 people and 1 group qshao jmccammon r2s2 ibuch McCammon
	CHARMM: The biomolecular simulation program [My Copy] Journal of Computational Chemistry, Vol. 30, No. 10. (30 July 2009), pp. 1545-1614. by B. R. R. Brooks, C. L. L. Brooks, A. D. D. Mackerell, et al.L. Nilsson, R. J. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. W. Pastor, C. B. B. Post, J. Z. Z. Pu, M. Schaefer, B. Tidor, R. M. M. Venable, H. L. L. Woodcock, X. Wu, W. Yang, D. M. M. York, M. Karplus posted to charmm molecular_dynamics by mmuecke on 2009-06-29 13:46:46 as along with 10 people and 1 group ckmyo dgront rodrigofaccioli medic0747 flbarroso jrperillaj xavierprat saravan sobolevnrm dimka baker-group
	Performance characterization of a molecular dynamics code on PC clusters: is there any easy parallelism in CHARMM? [My Copy] Parallel and Distributed Processing Symposium., Proceedings International, IPDPS 2002, Abstracts and CD-ROM In Parallel and Distributed Processing Symposium., Proceedings International, IPDPS 2002, Abstracts and CD-ROM (2002), pp. 30-37. by M. Taufer, E. Perathoner, A. Cavalli, A. Caflisch, T. Stricker posted to charmm molecular_dynamics by mmuecke on 2009-06-26 13:15:51 as
	Parametrization, Molecular Dynamics Simulation, and Calculation of Electron Spin Resonance Spectra of a Nitroxide Spin Label on a Polyalanine α-Helix [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 18. (1 May 2008), pp. 5755-5767. by Deniz Sezer, Jack H. Freed, Benoit Roux posted to charmm mtsl parametrization by yxue on 2009-06-16 01:03:55 as
	CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates, and Inositol [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Elizabeth R. Hatcher, Olgun Guvench, Alexander D. Mackerell posted to charmm parameterization by middledomain on 2009-05-06 18:36:49 as
	Validation of all-atom phosphatidylcholine lipid force fields in the tensionless NPT ensemble [My Copy] Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1788, No. 3. (1 March 2009), pp. 638-649. by J. Taylor, N. Whiteford, G. Bradley, G. Watson posted to analysis bilayer charmm dppc gromacs pdpc popc simulation by dimka on 2009-03-27 20:33:17 as along with 2 people and 1 group sobolevnrm paulschlesinger baker-group
	Algorithms for constrained molecular dynamics [My Copy] Journal of Computational Chemistry, Vol. 16, No. 10. (1995), pp. 1192-1209. by Eric Barth, Krzysztof Kuczera, Benedict Leimkuhler, Robert D. Skeel posted to charmm constraints molecular_dynamics shake by stephenbond on 2009-03-24 15:21:43 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 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
	Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Lennart Nilsson posted to charmm force_field by middledomain on 2008-12-20 16:02:58 as along with 1 person RamuAnandakrishnan
	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 charmm drude force_field polarizable by middledomain on 2008-12-20 15:22:45 as along with 1 person flbarroso
	Performance characteristics of biomolecular simulations on high-end systems with multi-core processors [My Copy] Parallel Computing, Vol. 34, No. 11. (November 2008), pp. 640-651. by S. Alam, P. Agarwal, J. Vetter posted to charmm high-performance_computing molecular_dynamics mpi multicore performance_analysis by mmuecke on 2008-11-19 11:50:14 as
	Assessing Atomistic and Coarse-Grained Force Fields for Protein−Lipid Interactions: the Formidable Challenge of an Ionizable Side Chain in a Membrane [My Copy] J. Phys. Chem. B (18 July 2008) by Igor Vorobyov, Libo Li, Toby W. Allen posted to charmm coarse-graining by softsimu on 2008-10-12 21:38:07 as along with 4 people loison A_Coletta_Thesis middledomain agrossfield
	Electrostatic Properties of Aqueous Salt Solution Interfaces: A Comparison of Polarizable and Nonpolarizable Ion Models [My Copy] J. Phys. Chem. B (20 August 2008) by Lee G. Warren, Sandeep Patel posted to charmm drude force_field ion polarization water by middledomain on 2008-08-20 12:00:10 as along with 1 person paulschlesinger
	CHARMMing: A New, Flexible Web Portal for CHARMM [My Copy] J. Chem. Inf. Model. (13 August 2008) by Benjamin T. Miller, Rishi P. Singh, Jeffery B. Klauda, Milan Hodošček, Bernard R. Brooks, Lee H. Woodcock posted to charmm web_interface by middledomain on 2008-08-13 13:11:15 as along with 3 people and 1 group yxue jmccammon reyez McCammon
	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 amber charmm comparison force_field gromos by middledomain on 2008-08-12 15:09:51 as along with 1 person agrossfield
	Improved Treatment of the Protein Backbone in Empirical Force Fields [My Copy] J. Am. Chem. Soc., Vol. 126, No. 3. (28 January 2004), pp. 698-699. by A. D. Mackerell, M. Feig, C. L. Brooks posted to charmm dipeptides force_field torsion by middledomain on 2008-08-01 09:31:27 as along with 1 person hlwoodcock
	Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations [My Copy] Journal of Computational Chemistry, Vol. 25, No. 11. (2004), pp. 1400-1415. by Alexander D. Mackerell, Michael Feig, Charles L. Brooks posted to ab_initio charmm dipeptides force_field by middledomain on 2008-08-01 09:30:33 as along with 4 people tovrstra mkrishna dgront hlwoodcock
	Is Alanine Dipeptide a Good Model for Representing the Torsional Preferences of Protein Backbones? [My Copy] J. Chem. Theory Comput. (30 July 2008) by Michael Feig posted to charmm dipeptide force_field md tip3p torsion by middledomain on 2008-07-30 13:37:23 as
	Effective energy function for proteins in solution. [My Copy] Proteins, Vol. 35, No. 2. (1 May 1999), pp. 133-152. by T. Lazaridis, M. Karplus posted to charmm eef1 by kgutwin on 2008-06-24 21:04:05 as along with 6 people and 2 groups melo_mcr oceanwind marcius bluvsh1 choonpeng hmk BioinfoCIPF SGU-CIPF
	Energetics of Infinite Homopolypeptide Chains: A New Look at Commonly Used Force Fields [My Copy] J. Phys. Chem. B (14 May 2008) by Evgeni Penev, Joel Ireta, Joan-Emma Shea posted to amber ameoba charmm comparison dft force_field opls by middledomain on 2008-05-14 09:46:35 as along with 1 person Vadikus
	Methyl Group Dynamics and the Onset of Anharmonicity in Myoglobin [My Copy] J. Phys. Chem. B (10 April 2008) by M. Krishnan, V. Kurkal-Siebert, J. C. Smith posted to charmm md methyl_rotation rotation torsion_paper by middledomain on 2008-04-10 14:01:14 as along with 3 people and 1 group barmak7282 mkrishna r2s2 CMB
	CHARMM-GUI: A web-based graphical user interface for CHARMM [My Copy] Journal of Computational Chemistry, Vol. 29, No. 11. (2008), pp. 1859-1865. by Sunhwan Jo, Taehoon Kim, Vidyashankara G. Iyer, Wonpil Im posted to charmm force_field gui web_interface by middledomain on 2008-03-20 13:06:34 as along with 1 person flbarroso
	Contribution of Charged Groups to the Enthalpic Stabilization of the Folded States of Globular Proteins [My Copy] J. Phys. Chem. B (28 February 2008) by V. M. Dadarlat, C. B. Post posted to charmm electrosatics enthalpy proteins solvation by middledomain on 2008-02-28 11:47:00 as
	Understanding the Dielectric Properties of Liquid Amides from a Polarizable Force Field [My Copy] J. Phys. Chem. B (27 February 2008) by E. Harder, V. M. Anisimov, T. Whitfield, A. D. Mackerell, B. Roux posted to charmm liquids polarization by middledomain on 2008-02-27 11:07:04 as along with 1 person and 1 group A_Coletta_Thesis Structural Biology Group TorVergata
	Hydrogen Bonding and Binding of Polybasic Residues with Negatively Charged Mixed Lipid Monolayers. [My Copy] Langmuir (23 January 2008) by Christian D. Lorenz, Jordi Faraudo, Alex Travesset posted to charmm dopc dops force-field lipid md membrane pip2 simulations by dimka on 2008-01-24 14:42:43 as along with 1 person priyaps
	Experimental validation of molecular dynamics simulations of lipid bilayers: a new approach. [My Copy] Biophysical journal, Vol. 88, No. 2. (1 February 2005), pp. 805-817. by Ryan W. Benz, Francisco Castro-Román, Douglas J. Tobias, Stephen H. White posted to charmm gromacs molecular-dynamics namd by softsimu on 2008-01-23 07:03:25 as along with 4 people loison sunnytov dimka nbrayali
	Development of a Polarizable Intermolecular Potential Function (PIPF) for Liquid Amides and Alkanes [My Copy] J. Chem. Theory Comput., Vol. 3, No. 6. (13 November 2007), pp. 1878-1889. by W. Xie, J. Pu, A. D. Mackerell, J. Gao posted to force_field polarization charmm by middledomain on 2008-01-22 16:58:06 as along with 2 people tovrstra loison
	Detailed analysis of grid-based molecular docking: A case study of CDOCKER - A CHARMm-based MD docking algorithm [My Copy] Journal of Computational Chemistry, Vol. 24, No. 13. (2003), pp. 1549-1562. by Guosheng Wu, Daniel H. Robertson, Charles L. Brooks, Michal Vieth posted to case_study charmm molecular_docking molecular_dynamics by mmuecke on 2008-01-21 14:31:48 as along with 5 people and 1 group oceanwind oteri apostola papatonyhill msuarezdiez Structural Biology Group TorVergata
	On the performance of molecular dynamics applications on current high-end systems. [My Copy] Philos Transact A Math Phys Eng Sci, Vol. 363, No. 1833. (15 August 2005), pp. 1987-1998. by J. Hein, F. Reid, L. Smith, I. Bush, M. Guest, P. Sherwood posted to charmm high-performance_computing molecular_dynamics survey by mmuecke on 2008-01-21 12:24:25 as along with 1 person hlwoodcock
	Monte Carlo simulations of biomolecules: The MC module in CHARMM [My Copy] Journal of Computational Chemistry, Vol. 27, No. 2. (30 January 2006), pp. 203-216. by Jie Hu, Ao Ma, Aaron R. Dinner posted to charmm dynamics molecular monte-carlo by msuarezdiez on 2008-01-16 12:44:28 as along with 1 person flbarroso
	Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations [My Copy] Journal of Computational Chemistry, Vol. 28, No. 9. (2007), pp. 1485-1502. by Lee H. Woodcock, Milan Hodo?&ccaron;ek, Andrew T. B. Gilbert, Peter M. W. Gill, Henry F. Schaefer, Bernard R. Brooks posted to charmm dynamics molecular by msuarezdiez on 2008-01-16 12:42:51 as
	Parallelizing Molecular Dynamics Programs for Distributed-Memory Machines [My Copy] IEEE Comput. Sci. Eng., Vol. 2, No. 2. (June 1995), pp. 18-29. by Yuan-Shin Hwang, Raja Das, Joel H. Saltz, Milan Hodoscek, Bernard R. Brooks posted to charmm high-performance_computing by mmuecke on 2007-12-11 10:11:54 as
	A consensus view of protein dynamics [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 3. (16 January 2007), pp. 796-801. by Manuel Rueda, Carles F. Costa, Tim Meyer, et al.Alberto Pérez, Jordi Camps, Adam Hospital, Josep, Modesto Orozco posted to protein_dynamics opls gromos force_field charmm amber by rabio on 2007-12-10 13:29:10 as along with 14 people and 1 group Diego_Prada bmduggan lna dimka aqeel aswin grahamc hmk zwang biehl Ema phoenixzxl ras LamBras The BMM Dome
	The development and integration of a distributed 3D FFT for a cluster of workstations [My Copy] In ALS'00: Proceedings of the 4th conference on 4th Annual Linux Showcase \& Conference, Atlanta (2000), pp. 26-26. by Christopher E. Cramer, John A. Board posted to charmm fft mpi by mmuecke on 2007-12-06 16:31:13 as
	Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field. [My Copy] J Med Chem, Vol. 49, No. 22. (2 November 2006), pp. 6596-6606. by A. Weis, K. Katebzadeh, P. Söderhjelm, I. Nilsson, U. Ryde posted to charmm mmpbsa by dimka on 2007-06-13 22:09:38 as
	Electrostatic Characterization of Enzyme Complexes: Evaluation of the Mechanism of Catalysis of Dihydrofolate Reductase [My Copy] J. Am. Chem. Soc., Vol. 119, No. 10. (12 March 1997), pp. 2386-2395. by W. R. Cannon, B. J. Garrison, S. J. Benkovic posted to charmm dhfr by ruvido on 2007-04-23 14:40:36 as
	Density of states simulations of proteins [My Copy] The Journal of Chemical Physics, Vol. 118, No. 9. (2003), pp. 4285-4290. by Nitin Rathore, Thomas A. Knotts, Juan J. de Pablo posted to charmm monte_carlo protein_thermodynamics wang-landau_sampling by rabio on 2007-02-27 14:03:44 as

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force_field	14
molecular_dynamics	14
md	7
amber	5
dynamics	4
field	4
force	4
molecular	4
comparison	3
force-field	3
gromos	3
high-performance_computing	3
polarization	3
development	2
dipeptide	2
dipeptides	2
drude	2
gromacs	2
lipid	2
molecular-dynamics	2
mpi	2
nmr	2
opls	2
parameterization	2
rna	2
simulation	2
torsion	2
web_interface	2
ab_initio	1
alanine	1
ameoba	1
analysis	1
bilayer	1
case_study	1
casp8	1
charmm27	1
coarse-graining	1
conformational	1
constraints	1
continuous_models	1
dft	1
dhfr	1
dna	1
dopc	1
dops	1
dppc	1
eef1	1
electrosatics	1
energy	1
enthalpy	1
error_analysis	1
experiments	1
fft	1
force-fields	1
forcefield	1
gpu	1
gui	1
hairpin	1
implicit-solvent	1
ion	1
lipids	1
liquids	1
membrane	1
methyl_rotation	1
mmpbsa	1
model	1
molecular_docking	1
monte-carlo	1
monte_carlo	1
mtsl	1
multicore	1
namd	1
p2	1
parametrization	1
pdpc	1
performance_analysis	1
pip2	1
plot	1
polarizable	1
popc	1
post-defense	1
potential	1
program	1
protein	1
protein_dynamics	1
protein_thermodynamics	1
proteins	1
qmmm	1
ramachandran	1
rotation	1
shake	1
simulations	1
solvation	1
survey	1
tip3p	1
torsion_paper	1
wang-landau_sampling	1
water	1

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