NDLI: ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics

Content Provider	ACM Digital Library
Author	Cickovski, Trevor Slabach, Thomas Ma, Qun Raeder, Troy Ko, Alice Nyerges, Matthew Izaguirre, Jesús A. Matthey, Thierry Hampton, Scott
Copyright Year	2004
Abstract	ProtoMol is a high-performance framework in C++ for rapid prototyping of novel algorithms for molecular dynamics and related applications. Its flexibility is achieved primarily through the use of inheritance and design patterns (object-oriented programming). Performance is obtained by using templates that enable generation of efficient code for sections critical to performance (generic programming). The framework encapsulates important optimizations that can be used by developers, such as parallelism in the force computation. Its design is based on domain analysis of numerical integrators for molecular dynamics (MD) and of fast solvers for the force computation, particularly due to electrostatic interactions. Several new and efficient algorithms are implemented in ProtoMol. Finally, it is shown that ProtoMol's sequential performance is excellent when compared to a leading MD program, and that it scales well for moderate number of processors. Binaries and source codes for Windows, Linux, Solaris, IRIX, HP-UX, and AIX platforms are available under open source license at http://protomol.sourceforge.net.
Starting Page	237
Ending Page	265
Page Count	29
File Format	PDF
ISSN	00983500
e-ISSN	15577295
DOI	10.1145/1024074.1024075
Volume Number	30
Issue Number	3
Journal	ACM Transactions on Mathematical Software (TOMS)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2004-09-01
Publisher Place	New York
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Fast electrostatic methods Incremental parallelism Molecular dynamics Multigrid Multiple time-stepping integration Object-oriented framework.
Content Type	Text
Resource Type	Article
Subject	Applied Mathematics Software

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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