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	GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 3. (1 March 2008), pp. 435-447. by B. Hess, C. Kutzner, D. van der Spoel, E. Lindahl posted to csproject gromacs md by r2s2 on 2008-04-12 02:56:10 as along with 22 people and 2 groups softsimu parnell rabio oteri krapnik robertvacha rodrigofaccioli pavanghatty janneb ZhangYinhe okapi flbarroso marceavi A_Coletta_Thesis choonpeng Lombardo_7 jwm daevans mmuecke sobolevnrm middledomain loison Structural Biology Group TorVergata baker-group
	Removing systematic errors in interionic potentials of mean force computed in molecular simulations using reaction-field-based electrostatics [My Copy] The Journal of Chemical Physics, Vol. 130, No. 10. (2009), 104106. by Andrij Baumketner posted to no-tag by r2s2 on 2009-10-18 04:21:10 as along with 1 person benlin
	A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field [My Copy] The Journal of Chemical Physics, Vol. 108, No. 24. (1998), pp. 10220-10230. by David van der Spoel, Paul J. van Maaren, Herman J. C. Berendsen posted to no-tag by r2s2 on 2009-10-18 04:19:37 as along with 3 people A_Coletta_Thesis jwagoner softsimu
	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 no-tag by r2s2 on 2009-10-18 04:19:20 as along with 3 people krapnik flbarroso choonpeng
	Molecular Dynamics Simulations of a Reversibly Folding β-Heptapeptide in Methanol: Influence of the Treatment of Long-Range Electrostatic Interactions [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 10. (12 March 2009), pp. 3112-3128. by Maria M. Reif, Vincent Kräutler, Mika A. Kastenholz, Xavier Daura, Philippe H. Hünenberger posted to no-tag by r2s2 on 2009-10-18 04:19:05 as
	Mechanism of Hg−C Protonolysis in the Organomercurial Lyase MerB [My Copy] Journal of the American Chemical Society, Vol. 131, No. 37. (23 September 2009), pp. 13278-13285. by Jerry M. Parks, Hong Guo, Cory Momany, et al.Liyuan Liang, Susan M. Miller, Anne O. Summers, Jeremy C. Smith posted to no-tag by r2s2 on 2009-10-04 02:16:34 as along with 1 person jmparks
	Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Roland Schulz, Benjamin Lindner, Loukas Petridis, Jeremy C. Smith posted to no-tag by r2s2 on 2009-10-01 04:17:20 as along with 1 person RamuAnandakrishnan
	Mechanical Properties of the Icosahedral Shell of Southern Bean Mosaic Virus: A Molecular Dynamics Study [My Copy] Vol. 96, No. 4. (18 February 2009), pp. 1350-1363. by Mareike Zink, Helmut Grubmüller posted to no-tag by r2s2 on 2009-07-21 18:30:20 as
	Ewald artifacts in computer simulations of ionic solvation and ion--ion interaction: A continuum electrostatics study [My Copy] The Journal of Chemical Physics, Vol. 110, No. 4. (1999), pp. 1856-1872. by Philippe H. Hünenberger, J. Andrew Mccammon posted to no-tag by r2s2 on 2009-07-21 16:40:04 as
	Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation [My Copy] The Journal of Physical Chemistry B, Vol. 104, No. 15. (1 April 2000), pp. 3668-3675. by Wolfgang Weber, Philippe H. Hunenberger, J. Andrew Mccammon posted to no-tag by r2s2 on 2009-07-21 16:39:59 as along with 1 person onufriev
	On the Ewald artifacts in computer simulations. The test-case of the octaalanine peptide with charged termini. [My Copy] Journal of biomolecular structure & dynamics, Vol. 23, No. 2. (October 2005), pp. 135-142. by M. A. Villarreal, G. G. Montich posted to no-tag by r2s2 on 2009-07-21 16:39:52 as
	Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study [My Copy] Biophysical Chemistry, Vol. 78, No. 1-2. (5 April 1999), pp. 69-88. by P. Hünenberger posted to no-tag by r2s2 on 2009-07-21 16:39:14 as along with 2 people scampos RamuAnandakrishnan
	LINCS: A linear constraint solver for molecular simulations [My Copy] Journal of Computational Chemistry, Vol. 18, No. 12. (1997), pp. 1463-1472. by Berk Hess, Henk Bekker, Herman J. C. Berendsen, Johannes G. E. M. Fraaije posted to no-tag by r2s2 on 2009-07-13 11:02:41 as along with 9 people kjell loison parnell dsmueller mijam A_Coletta_Thesis tji ashaytan jteyra
	Petascale Computing: Algorithms and Applications (Chapman & Hall/Crc Computational Science Series) [My Copy] (22 December 2007) posted to no-tag by r2s2 on 2009-07-13 09:39:30 as
	369 Tflop/s molecular dynamics simulations on the Roadrunner general-purpose heterogeneous supercomputer [My Copy] In SC '08: Proceedings of the 2008 ACM/IEEE conference on Supercomputing (2008), pp. 1-10. by Sriram Swaminarayan, Kai Kadau, Timothy C. Germann, Gordon C. Fossum posted to no-tag by r2s2 on 2009-07-12 20:13:46 as
	Electrostatics calculations: latest methodological advances. [My Copy] Current opinion in structural biology, Vol. 16, No. 2. (13 April 2006), pp. 142-151. by Patrice Koehl posted to no-tag by r2s2 on 2009-07-12 18:48:22 as along with 7 people oteri flbarroso LamBras BragilMassoud qwermish RamuAnandakrishnan jteyra
	Effects of long-range electrostatic forces on simulated protein folding kinetics [My Copy] Journal of Computational Chemistry, Vol. 29, No. 5. (2008), pp. 694-700. by Alex Robertson, Edgar Luttmann, Vijay S. Pande posted to no-tag by r2s2 on 2009-07-10 11:54:01 as along with 2 people and 1 group sobolevnrm RamuAnandakrishnan baker-group
	0.374 Pflop/s trillion-particle kinetic modeling of laser plasma interaction on Roadrunner [My Copy] In SC '08: Proceedings of the 2008 ACM/IEEE conference on Supercomputing (2008), pp. 1-11. by K. J. Bowers, B. J. Albright, B. Bergen, L. Yin, K. J. Barker, D. J. Kerbyson posted to no-tag by r2s2 on 2009-07-10 11:42:28 as
	Adapting a message-driven parallel application to GPU-accelerated clusters [My Copy] In SC '08: Proceedings of the 2008 ACM/IEEE conference on Supercomputing (2008), pp. 1-9. by James C. Phillips, John E. Stone, Klaus Schulten posted to no-tag by r2s2 on 2009-07-10 11:36:31 as along with 2 people naoya mamadoudiao
	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 no-tag by r2s2 on 2009-07-10 11:31:57 as along with 4 people and 1 group qshao jmccammon ibuch mmuecke McCammon
	Accelerating molecular dynamic simulation on graphics processing units [My Copy] Journal of Computational Chemistry, Vol. 30, No. 6. (2009), pp. 864-872. by Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, et al.Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande posted to no-tag by r2s2 on 2009-07-10 11:31:27 as along with 10 people and 3 groups anuragsethi kevinchannon flbarroso iantunbridge ihaque sobolevnrm ruvido massivemayhem barry RamuAnandakrishnan baker-group structural_bioinformatics McCammon
	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 no-tag by r2s2 on 2009-07-09 18:39:43 as along with 11 people and 1 group xdeupi agrossfield allmensch bmduggan apaydin kiekyon Borelli idoerg sobolevnrm edws paulschlesinger baker-group
	Charge-Based Interactions between Peptides Observed as the Dominant Force for Association in Aqueous Solution [My Copy] Angewandte Chemie International Edition, Vol. 47, No. 47. (10 November 2008), pp. 9059-9062. by Sylvia E. McLain, Alan k Soper, Isabella Daidone, Jeremy c Smith, Anthony Watts posted to no-tag by r2s2 on 2009-06-01 15:53:09 as
	High performance computing in biology: Multimillion atom simulations of nanoscale systems [My Copy] Journal of Structural Biology In Advances in Molecular Dynamics Simulations, Vol. 157, No. 3. (March 2007), pp. 470-480. by K. Y. Sanbonmatsu, C. S. Tung posted to no-tag by r2s2 on 2009-05-22 00:13:33 as along with 1 person dylan77
	Blue matter: approaching the limits of concurrency for classical molecular dynamics [My Copy] In SC '06: Proceedings of the 2006 ACM/IEEE conference on Supercomputing (2006) by Blake G. Fitch, Aleksandr Rayshubskiy, Maria Eleftheriou, et al.Christopher T. J. Ward, Mark Giampapa, Michael C. Pitman, Robert S. Germain posted to no-tag by r2s2 on 2009-05-20 16:50:25 as along with 1 person RamuAnandakrishnan
	Ten-microsecond MD simulation of a fast-folding WW domain [My Copy] Biophys. J. (13 March 2008), biophysj.108.131565. by Peter L. Freddolino, Feng Liu, Martin H. Gruebele, Klaus Schulten posted to no-tag by r2s2 on 2009-05-20 16:32:47 as along with 7 people and 1 group flbarroso doktornoe RamuAnandakrishnan paulschlesinger skoch3 samjlord biehl Koch_Lab
	Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus [My Copy] Structure, Vol. 14, No. 3. (March 2006), pp. 437-449. by Peter L. Freddolino, Anton S. Arkhipov, Steven B. Larson, Alexander Mcpherson, Klaus Schulten posted to no-tag by r2s2 on 2009-05-19 01:56:25 as along with 2 people and 2 groups barry RamuAnandakrishnan structural_bioinformatics Bioinformatics
	Scalable algorithms for molecular dynamics simulations on commodity clusters [My Copy] In SC '06: Proceedings of the 2006 ACM/IEEE conference on Supercomputing (2006) by Kevin J. Bowers, Edmond Chow, Huafeng Xu, et al.Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, Istvan Kolossvary, Mark A. Moraes, Federico D. Sacerdoti, John K. Salmon, Yibing Shan, David E. Shaw posted to no-tag by r2s2 on 2009-05-19 01:53:45 as along with 2 people mmuecke GermanErlenkamp
	GROMACS 3.0: a package for molecular simulation and trajectory analysis [My Copy] Journal of Molecular Modeling, Vol. 7, No. 8. (2001), pp. 306-317. by Erik Lindahl, Berk Hess, David van der Spoel posted to no-tag by r2s2 on 2009-05-15 15:24:16 as along with 8 people and 2 groups FilipeMaia janneb dsmueller choonpeng sebk rabio roland_ewald tji dIEMoSIRIS MoSi-Rostock
	GROMACS: fast, flexible, and free. [My Copy] J Comput Chem, Vol. 26, No. 16. (December 2005), pp. 1701-1718. by D. Van Der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, H. J. Berendsen posted to no-tag by r2s2 on 2009-05-15 15:23:54 as along with 18 people and 2 groups janneb dsmueller oteri choonpeng sebk dimka jwm ttjoseph bilab rabio Dinler tji softsimu ashaytan robertvacha sunnytov Diego_Prada A_Coletta_Thesis Radiation_Damage Stressosome
	Inclusion of reaction fields in molecular dynamics. Application to liquid water [My Copy] Faraday Discuss. Chem. Soc., Vol. 66 (1978), pp. 58-70. by Wilfred F. Gunsteren, Herman J. Berendsen, Johan A. Rullmann posted to rf by r2s2 on 2009-05-15 15:12:44 as
	A generalized reaction field method for molecular dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 102, No. 13. (1995), pp. 5451-5459. by Ilario G. Tironi, René Sperb, Paul E. Smith, Wilfred F. van Gunsteren posted to rf by r2s2 on 2009-05-15 15:12:34 as along with 3 people dsmueller RamuAnandakrishnan onufriev
	<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 no-tag by r2s2 on 2009-05-15 15:08:05 as along with 16 people ubcg08l flbarroso nickolay newton1234 kgutwin rpetrenko oceanwind RamuAnandakrishnan tovrstra dfgreen Lombardo_7 dgront mmuecke rabio saravan gisle
	VMD: Visual molecular dynamics [My Copy] Journal of Molecular Graphics, Vol. 14, No. 1. (February 1996), pp. 33-38. by W. Humphrey posted to no-tag by r2s2 on 2009-05-15 15:07:57 as along with 6 people and 1 group whitead csrocha pavanghatty choonpeng RamuAnandakrishnan tji Jiang Research Group
	Scalable molecular dynamics with NAMD [My Copy] Journal of Computational Chemistry, Vol. 26, No. 16. (December 2005), pp. 1781-1802. by James C. Phillips, Rosemary Braun, Wei Wang, et al.James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kalé, Klaus Schulten posted to no-tag by r2s2 on 2009-05-15 15:07:45 as along with 19 people and 5 groups pjkiley flbarroso yxue grondina rpetrenko oteri oceanwind dfgreen vahmurk gisle dimka jwm ttjoseph sangeetha yoel_rf bilab wilsoros sobolevnrm ibuch Radiation_Damage Stressosome Bioinformatics insilicodrug baker-group
	Polymorphic transitions in single crystals: A new molecular dynamics method [My Copy] Journal of Applied Physics, Vol. 52, No. 12. (1981), pp. 7182-7190. by M. Parrinello, A. Rahman posted to no-tag by r2s2 on 2009-05-15 15:04:38 as along with 2 people A_Coletta_Thesis ashaytan
	Canonical dynamics: Equilibrium phase-space distributions [My Copy] Physical Review A, Vol. 31, No. 3. (March 1985), 1695. by William G. Hoover posted to no-tag by r2s2 on 2009-05-15 15:04:26 as along with 3 people stephenbond and_ped10 OndrejMarsalek
	Molecular dynamics with coupling to an external bath [My Copy] The Journal of Chemical Physics, Vol. 81, No. 8. (1984), pp. 3684-3690. by H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. Dinola, J. R. Haak posted to no-tag by r2s2 on 2009-05-15 15:04:17 as along with 12 people and 1 group georgwachter A_Coletta_Thesis rdf dsmueller Lombardo_7 gsub lillekatt allmensch jwagoner tji choonpeng jteyra Structural Biology Group TorVergata
	P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation [My Copy] J. Chem. Theory Comput., Vol. 4, No. 1. (8 January 2008), pp. 116-122. by B. Hess posted to no-tag by r2s2 on 2009-05-15 15:04:07 as along with 2 people janneb choonpeng
	A modified TIP3P water potential for simulation with Ewald summation [My Copy] The Journal of Chemical Physics, Vol. 121, No. 20. (2004), pp. 10096-10103. by Daniel J. Price, Charles posted to tip3p by r2s2 on 2009-05-15 06:44:24 as along with 1 person softsimu
	Custom Assignment of MPI Ranks for Parallel Multi-dimensional FFTs: Evaluation of BG/P versus BG/L [My Copy] Parallel and Distributed Processing with Applications, 2008. ISPA '08. International Symposium on In Parallel and Distributed Processing with Applications, 2008. ISPA '08. International Symposium on (2008), pp. 271-283. by H. Jagode, J. Hein posted to no-tag by r2s2 on 2009-05-14 23:44:45 as
	Molecular Dynamics of the tRNAAla Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments [My Copy] The Journal of Physical Chemistry B, Vol. 106, No. 14. (1 April 2002), pp. 3696-3705. by Mafalda Nina, Thomas Simonson posted to no-tag by r2s2 on 2009-05-11 20:53:59 as
	Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal [My Copy] Proteins: Structure, Function, and Genetics, Vol. 43, No. 4. (2001), pp. 509-519. by Regula Walser, Philippe H. Hünenberger, Wilfred F. van Gunsteren posted to no-tag by r2s2 on 2009-05-11 20:53:45 as along with 1 person RamuAnandakrishnan
	Molecular dynamics simulation of highly charged proteins: comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions. [My Copy] Protein science : a publication of the Protein Society, Vol. 12, No. 10. (October 2003), pp. 2161-2172. by R. Gargallo, P. H. Hünenberger, F. X. Avilés, B. Oliva posted to rf by r2s2 on 2009-05-11 20:46:16 as
	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 r2s2 on 2009-05-08 19:21:12 as along with 11 people bmduggan rpetrenko robertvacha A_Coletta_Thesis mleis and_ped10 allmensch easybakemuffin 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 r2s2 on 2009-05-08 19:21:02 as along with 15 people and 2 groups jmparks rpetrenko A_Coletta_Thesis charris5 pavanghatty sobolevnrm choonpeng lillekatt and_ped10 easybakemuffin RamuAnandakrishnan ashaytan mikaellund 6rheology jteyra Structural Biology Group TorVergata baker-group
	Transition Networks: A Unifying Theme for Molecular Simulation and Computer Science [My Copy] Mathematical Modeling of Biological Systems, Volume I (2007), pp. 121-137. by Frank Noé, Jeremy C. Smith posted to no-tag by r2s2 on 2009-05-07 02:38:18 as along with 1 person barmak7282
	A fast multipole method combined with a reaction field for long-range electrostatics in molecular dynamics simulations: The effects of truncation on the properties of water [My Copy] The Journal of Chemical Physics, Vol. 118, No. 24. (2003), pp. 10847-10860. by Gerald Mathias, Bernhard Egwolf, Marco Nonella, Paul Tavan posted to no-tag by r2s2 on 2009-02-01 20:41:32 as
	Gaussian split Ewald: A fast Ewald mesh method for molecular simulation [My Copy] The Journal of Chemical Physics, Vol. 122, No. 5. (2005) by Yibing Shan, John L. Klepeis, Michael P. Eastwood, Ron O. Dror, David E. Shaw posted to no-tag by r2s2 on 2009-02-01 20:25:57 as along with 4 people charris5 stephenbond sjplimp ruvido
	Multiple grid methods for classical molecular dynamics [My Copy] Journal of Computational Chemistry, Vol. 23, No. 6. (2002), pp. 673-684. by Robert D. Skeel, Ismail Tezcan, David J. Hardy posted to no-tag by r2s2 on 2009-02-01 20:24:38 as along with 3 people dmitry_s_yershov stephenbond RamuAnandakrishnan

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