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BIOINFORMATICS
2007
53views more  BIOINFORMATICS 2007»
13 years 7 months ago
Wordom: a program for efficient analysis of molecular dynamics simulations
Michele Seeber, Marco Cecchini, Francesco Rao, Gio...
IPPS
2007
IEEE
14 years 1 months ago
Analysis of a Computational Biology Simulation Technique on Emerging Processing Architectures
1 Multi-paradigm, multi-threaded and multi-core computing devices available today provide several orders of magnitude performance improvement over mainstream microprocessors. These...
Jeremy S. Meredith, Sadaf R. Alam, Jeffrey S. Vett...
IPPS
2008
IEEE
14 years 1 months ago
Impact of multicores on large-scale molecular dynamics simulations
Processing nodes of the Cray XT and IBM Blue Gene Massively Parallel Processing (MPP) systems are composed of multiple execution units, sharing memory and network subsystems. Thes...
Sadaf R. Alam, Pratul K. Agarwal, Scott S. Hampton...
CPHYSICS
2008
106views more  CPHYSICS 2008»
13 years 7 months ago
A space-time-ensemble parallel nudged elastic band algorithm for molecular kinetics simulation
A scalable parallel algorithm has been designed to study long-time dynamics of many-atom systems based on the nudged elastic band method, which performs mutually constrained molec...
Aiichiro Nakano
JCC
2006
103views more  JCC 2006»
13 years 7 months ago
Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics
: The major bottleneck of today's atomistic molecular dynamics (MD) simulations is that because of the enormous computational effort involved, only processes at nanoseconds to...
Oliver F. Lange, Lars V. Schäfer, Helmut Grub...