Computer simulation of liquids
Computer simulation of liquids
Multilevel matrix multiplication and fast solution of integral equations
Journal of Computational Physics
Dangers of multiple time step methods
Journal of Computational Physics
Design patterns: elements of reusable object-oriented software
Design patterns: elements of reusable object-oriented software
ScaLAPACK user's guide
OOMPAA—object-oriented model for probing assemblages of atoms
Journal of Computational Physics - Special issue on computational molecular biophysics
NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
LAPACK Users' guide (third ed.)
LAPACK Users' guide (third ed.)
Lightweight computational steering of very large scale molecular dynamics simulations
Supercomputing '96 Proceedings of the 1996 ACM/IEEE conference on Supercomputing
Modern C++ design: generic programming and design patterns applied
Modern C++ design: generic programming and design patterns applied
The C++ Programming Language, Third Edition
The C++ Programming Language, Third Edition
Understanding Molecular Simulation
Understanding Molecular Simulation
Long time step molecular dynamics using targeted Langevin stabilization
Proceedings of the 2003 ACM symposium on Applied computing
Shadow hybrid Monte Carlo: an efficient propagator in phase space of macromolecules
Journal of Computational Physics
ProtoMol: a molecular dynamics research framework for algorithmic development
ICCS'03 Proceedings of the 2003 international conference on Computational science: PartIII
Shadow hybrid Monte Carlo: an efficient propagator in phase space of macromolecules
Journal of Computational Physics
GIPSE: Streamlining the Management of Simulation on the Grid
ANSS '05 Proceedings of the 38th annual Symposium on Simulation
Parallel multigrid summation for the N-body problem
Journal of Parallel and Distributed Computing
ProtoMol: a molecular dynamics research framework for algorithmic development
ICCS'03 Proceedings of the 2003 international conference on Computational science: PartIII
Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
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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.