Alice N. Ko  Home/Search
Context Related
| nd.edu/~izaguirr/papers/KOthesis.pdf Cached: PDF This document uses CoBlitz to cache paper downloads. If your firewall is blocking outgoing connections to port 3125, you can use these links to download local copies.
PS.gz PS Image Update HelpFrom: nd.edu/~izaguirr/w...publications (more) (Enter author homepages) |
Rate this article:      (best)Comment on this article |
Abstract: by Alice N. Ko Molecular dynamics (MD) for modeling the behavior of biological molecules is an important but di#cult task. This thesis presents an approach that incorporates ideas from recommender systems and automatic empirical optimization of software to simplify the tasks of setting up a computer model for MD and for choosing the optimal algorithm and parameters. It is intended to act as a guide for beginners to perform molecular modeling and also to present a concrete example; a program... (Update)
Cited by: More
PROTOMOL: A Molecular Dynamics Research - Framework For Algorithmic (2003) (Correct)
Targeted Mollified Impulse - A Multiscale Stochastic.. - Ma, Izaguirre (2003) (Correct)
Improved Sampling of Configuration Space of Biomolecules Using.. - Hampton (2004) (Correct)
Active bibliography (related documents): More All
2.0: Framework Design, Parallelization and Force Computation in.. - Matthey (Correct)
1.8: A Tutorial on the Prototyping of Multiple Time.. - Izaguirre.. (2001) (Correct)
1.5: Novel Multiscale Algorithms for Molecular Dynamics - Ma (2003) (Correct)
Similar documents based on text:
0.3: MDSimAid: A Recommender System for Automatic Parameter.. - Crocker, Hampton.. (2004) (Correct)
Related documents from co-citation: More All
5: Parallelization and Force Computation In Molecular Dynamics (context) - Matthey - 2002
5: PROTOMOL: an object-oriented framework for prototyping novel algorithms for mole.. - Matthey, Cickovski et al. - 2002
5: NAMD2 : Greater scalability for parallel molecular dynamics - Kale, Skeel et al. - 1998
BibTeX entry: (Update)
Ko, A.: MDSimAid: An automatic recommender for optimization of fast electrostatic algorithms for molecular simulations. Master's thesis, University of Notre Dame, Notre Dame, IN (2002) Available from http://www.nd.edu/izaguirr/papers/KOthesis.pdf. http://citeseer.ist.psu.edu/ko02mdsimaid.html More
@misc{ ko02mdsimaid,
author = "A. Ko",
title = "MDSimAid: An automatic recommender for optimization of fast electrostatic
algorithms for molecular simulations",
text = "Ko, A.: MDSimAid: An automatic recommender for optimization of fast electrostatic
algorithms for molecular simulations. Master's thesis, University of Notre
Dame, Notre Dame, IN (2002) Available from http://www.nd.edu/izaguirr/papers/KOthesis.pdf.",
year = "2002",
url = "citeseer.ist.psu.edu/ko02mdsimaid.html" }
Citations (may not include all citations):306 Computer Simulation of Liquids (context) - Allen, Tildesley - 1987
156 Computer Simulation Using Particles (context) - Hockney, Eastwood - 1981
120 Charmm: A program for macromolecular energy (context) - Brooks, Bruccoleri et al. - 1983
107 Principles of data mining (context) - Hand - 2001
94 The elements of statistical learning : data mining (context) - Hastie - 2001
56 Automated empirical optimizations of software and the ATLAS .. - Whaley, Petitet et al. - 2000
25 NAMD2: Greater scalability for parallel molecular dynamics - Kale, Skeel et al. - 1999
20 Pythia: A knowledge based system to select scientific algori.. - Weerawarana, Houstis et al. - 1996
18 Molecular Modelling: Principles and Applications (context) - Leach - 2001
15 Comparison of simple potential functions for simulating liqu.. (context) - Jorgensen, Chandrasekhar et al. - 1983
13 the convergence of a relaxation method with natural constrai.. (context) - Bakhvalov - 1966
12 Automated docking using a lamarckian genetic algorithm and a.. (context) - Morris, Goodsell et al. - 1998
11 Studies in molecular dynamics (context) - Alder, Wainwright - 1959
10 Principles of Fluorescence Spectroscopy (context) - Lakowicz - 1983
10 Phase transition for a hard sphere system (context) - Alder, Wainwright - 1957
10 A smooth particle mesh Ewald method (context) - Essmann, Perers et al. - 1995
9 Multiple grid methods for classical molecular dynamics (context) - Skeel, Tezcan et al. - 2002
9 Parallelization and Force Computation in Molecular Dynamics (context) - Matthey - 2002
8 ProtoMol: A molecular dynamics framework with incremental pa.. - Matthey, Izaguirre - 2001
8 How to mesh up Ewald sums (context) - Deserno, Holm - 1998
7 Ewald summation techniques in perspective: A survey (context) - Toukmaji, Jr - 1996
7 Principles of Protein X-Ray Crystallography (context) - Drenth - 1994
6 Optimized particle mesh Ewaldmultiple time step integration .. (context) - Case, particle et al. - 2001
6 Particle mesh Ewald: An N log (context) - Darden, York et al. - 1993
5 Dynamics of folded proteins (context) - McCammon, amd et al. - 1977
4 Ewald summation versus direct summation of shifted-force pot.. (context) - Brickmann, Dufner et al. - 1997
4 Ewald summation of electrostatic interactions in molecular d.. (context) - Gwozdz, Grzybowski et al. - 2000
4 Free energy via molecular simulation: Applications to chemic.. (context) - Beveridge, Di Capua - 1989
3 Structure available httphttpwww (context) - Wesson, the et al. - 1990
3 Fast Ewald sums for general van der Waals potentials (context) - Cagin, Chen et al. - 1997
3 Acceleration of the canonical molecular dynamics simulation .. - Kawata, Mikami - 1999
2 errors in the Ewald summation for dipolar systems (context) - Wang, Holm et al. - 2001
2 Computer simulation of a phospholipid monolayer-water system.. (context) - Alper, Bassolino et al. - 1993
2 a computer program for applying molecular mechanics (context) - Pearlman, Case et al. - 1995
2 Structure calculation of biological macromolecules from NMR .. (context) - Guntert - 1998
2 Multipole Ewald sums for the fast multipole method (context) - Schmidt, Lee - 1997
2 Ewald summation and multiple time step methods for molecular.. (context) - Komeiji - 2000
2 Molecular dynamics studies of solvated polypeptides: Why the.. (context) - Schreiber, Steinhauser - 1992
2 A relaxation method for solving elliptic di#erential equatio.. (context) - Fedorenko - 1961
2 Integrating computation and visualization for biomolecular a.. - Sanner, Duncan et al. - 1998
2 Mutational studies of protein structures and their stabiliti.. (context) - Shortle - 1992
2 ciency of the particle mesh Ewald method (context) - Petersen - 1995
1 A rigorous comparison of the Ewald method and the fast multi.. (context) - Petersen, Solvason et al. - 1995
1 Ewald summation and reaction field methods for potentials wi.. (context) - Nymand, Linse - 2000
1 The fast Fourier Possion method for calculating Ewald sums (context) - York, Yang - 1994
1 semi-refinement and fluid flow (context) - Hemker - 1995
1 ect of the treatment of longrange forces on the dynamics of .. (context) - Perera, Essmann et al. - 1995
1 cient multiple time step method for use with Ewald and parti.. (context) - Zhou, Harder et al. - 2001
1 How the unit cell surface charge distribution a#ects the ene.. (context) - Roberts, Schnitker - 1994
1 Python: A programming language for software integration and .. - Sanner - 1999
1 cient Ewald electrostatic calculations for large systems (context) - Smith, Pettitt - 1995
1 ects on protein stability (context) - Yang, Hong - 1992
1 All-atom empirical force field for nucleic acids: 1) Paramet.. (context) - Foloppe, Jr - 2000
1 Comparison of protein models minimized by the all-atom and u.. (context) - Kini, Eveans - 1992
1 Calculation of electrostatic potentials in an enzyme active .. (context) - Gilson, Honig - 1987
1 Structure Elucidation by NMR in Organic Chemistry - A Practi.. (context) - Breitmaier - 1993
1 IR Spectroscopy: An Introduction (context) - Gunzler, Gremlich et al. - 2002
1 the truncation of long-range electrostatic interactions in D.. (context) - Norberg, Nilsson - 2000
1 A simple test for evaluating the truncation e#ects in simula.. (context) - Au, Beveridge - 1995
1 ects of long-range interactions on the dynamics of ions in a.. (context) - Buono, Cohen et al. - 1994
1 Computer simulation study of the mean forces between ferrous.. (context) - Bader, Chandler - 1992
http://storm.ameslab.gov/
Documents on the same site (http://www.nd.edu/~izaguirr/webpage_files/publications.htm): More
Novel Multiscale Algorithms for Molecular Dynamics - Ma (2003) (Correct)
MDSimAid: A Recommender System for Automatic Parameter.. - Crocker, Hampton.. (2004) (Correct)
GIPSE: A Toolset for Streamlining the Management.. - Striegel, Shorts, .. (Correct)
Online articles have much greater impact More about CiteSeer.IST Add search form to your site Submit documents Feedback
CiteSeer.IST - Copyright Penn State and NEC