Literature DB >> 11939600

Multiple grid methods for classical molecular dynamics.

Robert D Skeel1, Ismail Tezcan, David J Hardy.   

Abstract

Presented in the context of classical molecular mechanics and dynamics are multilevel summation methods for the fast calculation of energies/forces for pairwise interactions, which are based on the hierarchical interpolation of interaction potentials on multiple grids. The concepts and details underlying multigrid interpolation are described. For integration of molecular dynamics the use of different time steps for different interactions allows longer time steps for many of the interactions, and this can be combined with multiple grids in space. Comparison is made to the fast multipole method, and evidence is presented suggesting that for molecular simulations multigrid methods may be superior to the fast multipole method and other tree methods.

Mesh:

Year:  2002        PMID: 11939600     DOI: 10.1002/jcc.10072

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  24 in total

1.  Ewald mesh method for quantum mechanical calculations.

Authors:  Chun-Min Chang; Yihan Shao; Jing Kong
Journal:  J Chem Phys       Date:  2012-03-21       Impact factor: 3.488

2.  Calculation of absolute protein-ligand binding affinity using path and endpoint approaches.

Authors:  Michael S Lee; Mark A Olson
Journal:  Biophys J       Date:  2005-11-11       Impact factor: 4.033

3.  Scalable molecular dynamics with NAMD.

Authors:  James C Phillips; Rosemary Braun; Wei Wang; James Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D Skeel; Laxmikant Kalé; Klaus Schulten
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

4.  Multilevel Summation of Electrostatic Potentials Using Graphics Processing Units.

Authors:  David J Hardy; John E Stone; Klaus Schulten
Journal:  Parallel Comput       Date:  2009-03-01       Impact factor: 0.986

5.  NONUNIFORM FOURIER TRANSFORMS FOR RIGID-BODY AND MULTI-DIMENSIONAL ROTATIONAL CORRELATIONS.

Authors:  Chandrajit Bajaj; Benedikt Bauer; Radhakrishna Bettadapura; Antje Vollrath
Journal:  SIAM J Sci Comput       Date:  2013-07-01       Impact factor: 2.373

Review 6.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

7.  Correcting Mesh-Based Force Calculations to Conserve Both Energy and Momentum in Molecular Dynamics Simulations.

Authors:  Robert D Skeel; David J Hardy; James C Phillips
Journal:  J Comput Phys       Date:  2007-07-01       Impact factor: 3.553

8.  Molecular modeling of nucleic acid structure: electrostatics and solvation.

Authors:  T E Cheatham; B R Brooks; P A Kollman
Journal:  Curr Protoc Nucleic Acid Chem       Date:  2001-08

Review 9.  Biomolecularmodeling and simulation: a field coming of age.

Authors:  Tamar Schlick; Rosana Collepardo-Guevara; Leif Arthur Halvorsen; Segun Jung; Xia Xiao
Journal:  Q Rev Biophys       Date:  2011-05       Impact factor: 5.318

10.  TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.

Authors:  Josh V Vermaas; David J Hardy; John E Stone; Emad Tajkhorshid; Axel Kohlmeyer
Journal:  J Chem Inf Model       Date:  2016-06-01       Impact factor: 4.956

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