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OndrejMarsalek's library [67 articles]

Recent papers added to OndrejMarsalek's library ordered by importance.
  • Embedded divide-and-conquer algorithm on hierarchical real-space grids: parallel molecular dynamics simulation based on linear-scaling density functional theory
    Computer Physics Communications, Vol. 167, No. 3. (1 May 2005), pp. 151-164.
    by Fuyuki Shimojo, Rajiv K Kalia, Aiichiro Nakano, Priya Vashishta
    posted to check by OndrejMarsalek on 2008-04-28 19:16:02 as **** along with 1 person voronov
  • notes Canonical dynamics: Equilibrium phase-space distributions
    Physical Review A, Vol. 31, No. 3. (March 1985), 1695.
    by William G Hoover
    posted to algorithms masters md by OndrejMarsalek on 2008-04-02 10:22:24 as **** along with 1 person and_ped10
  • Statistical thermodynamics in the classical molecular dynamics ensemble. III. Numerical results
    The Journal of Chemical Physics, Vol. 100, No. 4. (1994), pp. 3068-3078.
    by Rolf Lustig
    posted to check by OndrejMarsalek on 2008-03-29 14:54:27 as ****
  • Harvesting graphics power for MD simulations
    (20 Sep 2007)
    by JA van Meel, A Arnold, D Frenkel, Portegies SF Zwart, RG Belleman
    posted to cuda md software by OndrejMarsalek on 2008-03-01 17:40:55 as ****
  • Accelerating molecular modeling applications with graphics processors.
    J Comput Chem (25 September 2007)
    by John E E Stone, James C C Phillips, Peter L L Freddolino, David J J Hardy, Leonardo G G Trabuco, Klaus Schulten
    posted to cuda electrostatics md software by OndrejMarsalek on 2008-03-01 17:38:55 as **** along with 7 people and 1 group npt11tpn afenley BragilMassoud ruvido sobolevnrm yalexeev mikaellund baker-group
  • Molecular Dynamics Simulations on Commodity GPUs with CUDA
    High Performance Computing – HiPC 2007 (2007), pp. 185-196.
    by Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Müller-Wittig
    posted to cuda md software by OndrejMarsalek on 2008-03-01 17:35:33 as **** along with 1 person stumbled
  • General Purpose Molecular Dynamics Simulations Fully Implemented on Graphics Processing Units
    Journal of Computational Physics, Vol. In Press, Accepted Manuscript
    by Joshua A Anderson, Chris D Lorenz, A Travesset
    posted to cuda md software by OndrejMarsalek on 2008-03-01 17:34:33 as ****
  • Local electrostatics algorithm for classical molecular dynamics simulations
    The Journal of Chemical Physics, Vol. 127, No. 13. (2007)
    by Jörg Rottler
    posted to algorithms electrostatics md by OndrejMarsalek on 2008-02-06 10:13:26 as **** along with 5 people and 1 group sobolevnrm afenley softsimu mikaellund michaelbussmann baker-group
  • A Case Study in High-Performance Mixed-Language Programming
    Applied Parallel Computing. State of the Art in Scientific Computing (2007), pp. 36-49.
    by Hans Langtangen
    posted to software by OndrejMarsalek on 2008-02-05 11:12:50 as ****
  • A new leapfrog integrator of rotational motion. The revised angular-momentum approach
    (18 Jan 1999)
    by Igor P Omelyan
    posted to check by OndrejMarsalek on 2008-04-05 13:05:05 as ***
  • Computer Simulation of Liquids
    (29 June 1989)
    by MP Allen, DJ Tildesley
    posted to book masters md by OndrejMarsalek on 2008-03-16 23:04:45 as *** along with 3 people kkims agupta0318 mikaellund
  • Understanding Molecular Simulation (Computational Science Series, Vol 1)
    (15 October 2001)
    by Daan Frenkel, B Smit
    posted to book masters md by OndrejMarsalek on 2008-03-16 23:03:20 as *** along with 3 people kkims ptupper mikaellund
  • Faunus: an objected oriented framework for molecular simulation.
    Source Code Biol Med, Vol. 3, No. 1. (1 February 2008)
    by Mikael Lund, Martin Trulsson, Bjorn Persson
    posted to algorithms software by OndrejMarsalek on 2008-02-06 18:33:11 as *** along with 1 person mikaellund
  • Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics
    The Journal of Chemical Physics, Vol. 124, No. 23. (2006)
    by Christopher J Fennell, Daniel J Gezelter
    posted to algorithms electrostatics md by OndrejMarsalek on 2008-02-04 22:15:06 as *** along with 3 people and 1 group sobolevnrm mikaellund michaelbussmann baker-group
  • Canonical sampling through velocity rescaling
    The Journal of Chemical Physics, Vol. 126, No. 1. (2007)
    by Giovanni Bussi, Davide Donadio, Michele Parrinello
    posted to algorithms md by OndrejMarsalek on 2008-02-04 22:14:21 as *** along with 2 people daevans michaelbussmann
  • notes A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters
    The Journal of Chemical Physics, Vol. 76, No. 1. (1982), pp. 637-649.
    by William C Swope, Hans C Andersen, Peter H Berens, Kent R Wilson
    posted to algorithms masters md numerics by OndrejMarsalek on 2008-03-30 19:31:14 as **
  • notes A Modified Tree Code Don't Laugh: It Runs
    Journal of Computational Physics, Vol. 87 (March 1990), 161.
    by JE Barnes
    posted to algorithms masters treecode by OndrejMarsalek on 2008-02-28 16:37:42 as **
  • An Efficient Program for Many-Body Simulation
    SIAM Journal on Scientific and Statistical Computing, Vol. 6, No. 1. (1985), pp. 85-103.
    by Andrew W Appel
    posted to algorithms electrostatics masters plasma treecode by OndrejMarsalek on 2008-02-28 16:23:43 as **
  • notes P3M3DP-The three-dimensional periodic particle-particle/ particle-mesh program
    Computer Physics Communications, Vol. 19 (April 1980), pp. 215-261.
    by JW Eastwood, RW Hockney, DN Lawrence
    posted to algorithms electrostatics masters plasma by OndrejMarsalek on 2008-02-28 16:09:37 as ** along with 1 person michaelbussmann
  • notes Some Multistep Methods for Use in Molecular Dynamics Calculations
    Journal of Computational Physics, Vol. 20 (February 1976), 130.
    by D Beeman
    posted to algorithms masters md numerics by OndrejMarsalek on 2008-02-28 15:48:02 as **
  • Numerical Recipes: The Art of Scientific Computing
    (01 August 2007)
    by William H Press, Saul A Teukolsky, William T Vetterling, Brian P Flannery
    posted to algorithms book masters numerics by OndrejMarsalek on 2008-02-16 19:48:02 as ** along with 9 people and 1 group diancu ansobol sobolevnrm mshafiei 6rheology mmeteo chitah Zaphod seana baker-group
  • Averaged Configurations from Molecular Dynamics Simulations
    Applied Parallel Computing. State of the Art in Scientific Computing (2007), pp. 51-58.
    by K Gillis, J Vatamanu, M Razul, Peter Kusalik
    posted to algorithms md by OndrejMarsalek on 2008-02-05 11:20:08 as ** along with 1 person michaelbussmann
  • A High Performance Generic Scientific Simulation Environment
    Applied Parallel Computing. State of the Art in Scientific Computing (2007), pp. 996-1005.
    by René Heinzl, Michael Spevak, Philipp Schwaha, Siegfried Selberherr
    posted to software by OndrejMarsalek on 2008-02-05 11:12:26 as ** along with 1 person michaelbussmann
  • P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation
    J. Chem. Theory Comput., Vol. 4, No. 1. (8 January 2008), pp. 116-122.
    by B Hess
    posted to algorithms gromacs md by OndrejMarsalek on 2008-02-04 22:16:01 as **
  • Základy fysikálních měření (II)B (in Czech)
    (1974)
    by Jaromír Brož
    posted to masters by OndrejMarsalek on 2008-04-01 18:24:57 as *
  • notes Potential calculation and some applications
    Methods Comput. Phys. (1970)
    by RW Hockney
    posted to algorithms masters by OndrejMarsalek on 2008-03-30 19:58:40 as *
  • Partial Differential Equations
    (22 December 1994)
    by DiBenedetto, Emmanuele
    posted to book masters math by OndrejMarsalek on 2008-03-24 14:41:17 as *
  • Die Berechnung optischer und elektrostatischer Gitterpotentiale
    Annalen der Physik, Vol. 369, No. 3. (1921), pp. 253-287.
    by PP Ewald
    posted to algorithms electrostatics masters by OndrejMarsalek on 2008-03-18 12:46:16 as * along with 1 person softsimu
  • Langmuir probe technique
    General Electric Rev, Vol. 27 (1924)
    by I Langmuir, Mott H Smith
    posted to masters plasma by OndrejMarsalek on 2008-03-15 21:28:58 as *
  • notes An Unsymmetric-Pattern Multifrontal Method for Sparse LU Factorization
    SIAM Journal on Matrix Analysis and Applications, Vol. 18, No. 1. (1997), pp. 140-158.
    by Timothy A Davis, Iain S Duff
    posted to masters numerics by OndrejMarsalek on 2008-03-01 17:55:51 as *
  • notes A combined unifrontal/multifrontal method for unsymmetric sparse matrices
    ACM Trans. Math. Softw., Vol. 25, No. 1. (March 1999), pp. 1-20.
    by Timothy A Davis, Iain S Duff
    posted to masters numerics by OndrejMarsalek on 2008-03-01 17:54:05 as *
  • notes Algorithm 832: UMFPACK V4.3---an unsymmetric-pattern multifrontal method
    ACM Trans. Math. Softw., Vol. 30, No. 2. (June 2004), pp. 196-199.
    by Timothy A Davis
    posted to masters numerics by OndrejMarsalek on 2008-03-01 17:52:50 as * along with 1 person bamberg
  • notes A column pre-ordering strategy for the unsymmetric-pattern multifrontal method
    ACM Trans. Math. Softw., Vol. 30, No. 2. (June 2004), pp. 165-195.
    by Timothy A Davis
    posted to masters numerics by OndrejMarsalek on 2008-03-01 17:51:57 as *
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