Tag gromacs [33 articles] Export

Recent papers classified by the tag gromacs.

	GROMACS: fast, flexible, and free. [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1701-1718. by David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. Berendsen posted to gromacs by arifor on 2009-11-19 16:18:41 as along with 20 people and 2 groups krapnik r2s2 janneb dsmueller oteri choonpeng sebk dimka jwm ttjoseph bilab rabio Dinler tji softsimu ashaytan robertvacha sunnytov Diego_Prada A_Coletta_Thesis Radiation_Damage Stressosome
	jSimMacs for GROMACS: A Java Application for Advanced Molecular Dynamics Simulations with Remote Access Capability [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 10. (26 October 2009), pp. 2412-2417. by Sanjit Roopra, Bernhard Knapp, Ulrich Omasits, Wolfgang Schreiner posted to user_interface molecular_dynamics_simulations jsimmacs gui gromacs by diamantis on 2009-11-03 03:46:48 as
	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 Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl posted to gromacs by softsimu on 2009-10-03 18:18:18 as along with 24 people and 2 groups mikaellund sunnytov parnell rabio oteri krapnik robertvacha rodrigofaccioli pavanghatty janneb ZhangYinhe okapi flbarroso marceavi A_Coletta_Thesis choonpeng Lombardo_7 jwm daevans mmuecke sobolevnrm r2s2 middledomain loison Structural Biology Group TorVergata baker-group
	A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations [My Copy] Journal of Computational Chemistry, Vol. 22, No. 5. (2001), pp. 501-508. by Vincent Kräutler, Wilfred F. van Gunsteren, Philippe H. Hünenberger posted to shake gromacs by dimka on 2009-10-03 07:17:41 as
	Polypeptide Friction and Adhesion on Hydrophobic and Hydrophilic Surfaces: A Molecular Dynamics Case Study [My Copy] Journal of the American Chemical Society In Journal of the American Chemical Society, Vol. 130, No. 37. (17 September 2008), pp. 12408-12413. by Andreas Serr, Dominik Horinek, Roland R. Netz posted to gromacs friction by qshao on 2009-09-08 18:20:24 as along with 2 people loison paulschlesinger
	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 gromacs by loison on 2009-09-04 13:05:55 as along with 11 people trishul sunnytov kjell parnell r2s2 dsmueller mijam A_Coletta_Thesis tji ashaytan jteyra
	Exploring the Helix-Coil Transition via All-Atom Equilibrium Ensemble Simulations [My Copy] Biophysical Journal, Vol. 88, No. 4. (1 April 2005), pp. 2472-2493. by Eric J. Sorin, Vijay S. Pande posted to acid amber gromacs md nucleic by dsmueller on 2009-05-11 22:08:47 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
	Hybrid atomistic-continuum methods for multiscale hydrodynamics [My Copy] (26 Oct 2003) by Hettithanthrige S. Wijesinghe, Nicolas G. Hadjiconstantinou posted to gromacs md modeling multiscale by ZhangYinhe on 2009-03-26 12:30:19 as
	An Improved United Atom Force Field for Simulation of Mixed Lipid Bilayers [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 9. (5 March 2009), pp. 2748-2763. by See-Wing Chiu, Sagar A. Pandit, H. L. Scott, Eric Jakobsson posted to fields force gromacs by loison on 2009-03-19 08:44:41 as along with 1 person and 1 group sobolevnrm baker-group
	Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel [My Copy] PLoS Comput Biol, Vol. 5, No. 2. (20 February 2009), e1000289. by Pär Bjelkmar, Perttu S. Niemelä, Ilpo Vattulainen, Erik Lindahl posted to gromacs kv12 popc popg simulation by dimka on 2009-02-24 22:51:28 as along with 2 people Vadikus blasco_morozzo
	Toward a Coarse-Grained Protein Model Coupled with a Coarse-Grained Solvent Model: Solvation Free Energies of Amino Acid Side Chains [My Copy] Journal of Chemical Theory and Computation In Journal of Chemical Theory and Computation, Vol. 4, No. 11. (11 November 2008), pp. 1891-1901. by Wei Han, Cheuk-Kin Wan, Yun-Dong Wu posted to coarse-grained field force gromacs modeling parameter solvent thermodynamics water by rbaron on 2008-12-05 18:49:52 as along with 4 people loison sunrise agrossfield middledomain
	Molecular motions of human cyclin-dependent kinase 2. [My Copy] J Biol Chem, Vol. 280, No. 14. (8 April 2005), pp. 13993-14005. by C. P. Barrett, M. E. Noble posted to gromacs kinase md by timg on 2008-10-29 09:48:32 as along with 2 people aqeel gloria
	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 gromacs by robertvacha on 2008-09-21 15:11:26 as along with 13 people anallam sunnytov bmduggan rpetrenko r2s2 A_Coletta_Thesis mleis and_ped10 allmensch easybakemuffin RamuAnandakrishnan tji ashaytan
	Flooding in <TT>GROMACS</TT>: Accelerated barrier crossings in molecular dynamics [My Copy] Journal of Computational Chemistry, Vol. 27, No. 14. (2006), pp. 1693-1702. by Oliver F. Lange, Lars V. Schäfer, Helmut Grubmüller posted to gromacs by softsimu on 2008-09-16 09:52:21 as along with 2 people daevans loison
	Speeding up parallel GROMACS on high-latency networks [My Copy] Journal of Computational Chemistry, Vol. 28, No. 12. (2007), pp. 2075-2084. by Carsten Kutzner, David van der Spoel, Martin Fechner, et al.Erik Lindahl, Udo W. Schmitt, Bert L. De Groot, Helmut Grubmüller posted to gromacs by softsimu on 2008-09-16 09:50:28 as
	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 gromacs by jteyra on 2008-08-20 10:44:22 as along with 16 people and 2 groups krapnik jmparks rpetrenko A_Coletta_Thesis r2s2 charris5 pavanghatty sobolevnrm choonpeng lillekatt and_ped10 easybakemuffin RamuAnandakrishnan ashaytan mikaellund 6rheology Structural Biology Group TorVergata baker-group
	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 gromacs by jteyra on 2008-08-20 10:43:44 as along with 12 people and 1 group georgwachter A_Coletta_Thesis rdf r2s2 dsmueller Lombardo_7 gsub lillekatt allmensch jwagoner tji choonpeng Structural Biology Group TorVergata
	Lipid Bilayers Driven to a Wrong Lane in Molecular Dynamics Simulations by Subtle Changes in Long-Range Electrostatic Interactions [My Copy] J. Phys. Chem. B, Vol. 108, No. 14. (8 April 2004), pp. 4485-4494. by M. Patra, M. Karttunen, M. T. Hyvonen, E. Falck, I. Vattulainen posted to dppc gromacs md simulations by dimka on 2008-06-27 04:38:49 as along with 1 person softsimu
	Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models [My Copy] Journal of Computational Chemistry, Vol. 13, No. 8. (1992), pp. 952-962. by Shuichi Miyamoto, Peter A. Kollman posted to gromacs md by robertvacha on 2008-06-20 17:19:49 as along with 8 people oteri Lombardo_7 choonpeng A_Coletta_Thesis jwagoner tji softsimu ashaytan
	GROMACS: A message-passing parallel molecular dynamics implementation [My Copy] Computer Physics Communications, Vol. 91, No. 1-3. (02 September 1995), pp. 43-56. by H. Berendsen posted to gromacs by robertvacha on 2008-06-20 17:11:56 as along with 7 people trishul xiaoshijun janneb choonpeng ffranca tji gisle
	Molecular Dynamics Simulations of Water with Novel Shell-Model Potentials [My Copy] J. Phys. Chem. B, Vol. 105, No. 13. (5 April 2001), pp. 2618-2626. by P. J. van Maaren, D. van der Spoel posted to gromacs polarizability by softsimu on 2008-06-17 18:21:28 as along with 1 person alex_bunker
	A common, avoidable source of error in molecular dynamics integrators [My Copy] The Journal of Chemical Physics, Vol. 126, No. 4. (2007) by Ross A. Lippert, Kevin J. Bowers, Ron O. Dror, et al.Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, Istvan Kolossvary, David E. Shaw posted to gromacs by loison on 2008-05-23 10:40:13 as along with 1 person softsimu
	Molecular Dynamics Study of Ion Transfer and Distribution at the Interface of Water and 1,2-Dichlorethane [My Copy] J. Phys. Chem. C, Vol. 112, No. 3. (24 January 2008), pp. 647-649. by C. D. Wick, L. X. Dang posted to gromacs ion transfer by bentenin on 2008-02-09 21:43:35 as
	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 3 people sunnytov dimka nbrayali
	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 gromacs by tji on 2007-12-11 08:05:05 as along with 9 people and 2 groups trishul FilipeMaia r2s2 janneb dsmueller choonpeng sebk rabio roland_ewald dIEMoSIRIS MoSi-Rostock
	A generalized born implicit-membrane representation compared to experimental insertion free energies. [My Copy] Biophys J, Vol. 92, No. 7. (1 April 2007), pp. 2338-2349. by M. B. Ulmschneider, J. P. Ulmschneider, M. S. Sansom, A. Di Nola posted to gb gromacs implicit-membrane md membrane-effect by dimka on 2007-05-18 22:24:45 as along with 1 person onufriev
	Exploring the Helix-Coil Transition via All-Atom Equilibrium Ensemble Simulations. [My Copy] Biophys J, Vol. 88, No. 4. (April 2005), pp. 2472-2493. by E. J. Sorin, V. S. Pande posted to amber forcefields gromacs by loison on 2006-11-03 18:41:21 as along with 4 people paulymer krapnik ttjoseph allmensch
	Molecular Dynamics Simulation of the Kinetics of Spontaneous Micelle Formation [My Copy] J. Phys. Chem. B, Vol. 104, No. 51. (28 December 2000), pp. 12165-12173. by S. J. Marrink, D. P. Tieleman, A. E. Mark posted to dpc gromacs phasediagram solvent by loison on 2006-10-16 08:19:55 as
	Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid–protein interactions, side chain transfer free energies and model proteins [My Copy] Journal of Physics: Condensed Matter, Vol. 18, No. 28. (2006), pp. S1221-S1234. by Peter D. Tieleman, Justin L. Maccallum, Walter L. Ash, Christian Kandt, Zhitao Xu, Luca Monticelli posted to gromacs solvent theory tip5p water by loison on 2006-10-13 21:58:42 as along with 2 people arnaucordomi sunnytov
	Experimental and Theoretical Investigation of the Micellar-Assisted Solubilization of Ibuprofen in Aqueous Media [My Copy] Langmuir, Vol. 22, No. 4. (14 February 2006), pp. 1514-1525. by B. C. Stephenson, C. O. Rangel-Yagui, A. P. Junior, L. C. Tavares, K. Beers, D. Blankschtein posted to gromacs sds simulation by loison on 2006-10-10 14:57:40 as along with 1 person softsimu
	Comparative study of generalized Born models: protein dynamics. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 19. (10 May 2005), pp. 6760-6764. by H. Fan, A. E. Mark, J. Zhu, B. Honig posted to generalized-born gromacs by ttjoseph on 2006-03-13 05:22:58 as along with 1 person krapnik
	Development of the force field parameters for phosphoimidazole and phosphohistidine. [My Copy] J Comput Chem, Vol. 25, No. 11. (August 2004), pp. 1313-1321. by Y. A. Kosinsky, P. E. Volynsky, P. Lagant, et al.G. Vergoten, E. Suzuki, A. S. Arseniev, R. G. Efremov posted to ab-initio development force-field gromacs imidazole methodology pho-his by dimka on 2005-12-16 22:28:57 as along with 1 person and 1 group A_Coletta_Thesis Structural Biology Group TorVergata

Note: You may cite this page as: http://www.citeulike.org/tag/gromacs

md	12
simulation	6
molecular-dynamics	4
molecular_dynamics	3
pads	3
solvent	3
spatial-simulation	3
amber	2
charmm	2
dppc	2
force	2
modeling	2
popc	2
simulations	2
water	2
82c24-dynamic-interface	1
92e10-molecular-structure	1
ab-initio	1
acid	1
analysis	1
bilayer	1
coarse-grained	1
conformational_flooding	1
csproject	1
development	1
dpc	1
dynamics	1
field	1
fields	1
force-field	1
force_field	1
forcefields	1
friction	1
gb	1
generalized-born	1
gui	1
imidazole	1
implicit-membrane	1
ion	1
jsimmacs	1
kinase	1
kv12	1
membrane-effect	1
methodology	1
molecular	1
molecular_dynamics_simulations	1
multiscale	1
namd	1
nucleic	1
parameter	1
pdpc	1
phasediagram	1
pho-his	1
pla	1
polarizability	1
popg	1
problems-diffusion-limited-aggregation	1
qmmm	1
sds	1
shake	1
theory	1
thermodynamics	1
tip5p	1
transfer	1
user_interface	1

Tag gromacs [33 articles] Export

Related Tags