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VMD: visual molecular dynamics.
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Scalable molecular dynamics with NAMD
NAMD is a parallel molecular dynamics code designed for high‐performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high‐end parallel platforms, as well as…
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'Neural-gas' network for vector quantization and its application to time-series prediction
TLDR
It is shown that the dynamics of the reference (weight) vectors during the input-driven adaptation procedure are determined by the gradient of an energy function whose shape can be modulated through a neighborhood determining parameter and resemble the dynamicsof Brownian particles moving in a potential determined by a data point density.
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NAMD2: Greater Scalability for Parallel Molecular Dynamics
TLDR
The NAMD2 program is presented, which uses spatial decomposition combined with force decomposition to enhance scalability and modularly organized, and implemented using Charm++, a parallel C++ dialect, so as to enhance its modifiability.
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A model for photoreceptor-based magnetoreception in birds.
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Topology representing networks
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Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
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The crystal structure of the light-harvesting complex II (B800-850) from Rhodospirillum molischianum.
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Neural computation and self-organizing maps - an introduction
A process for removing sulfur from crude oil by contacting with calcium carbonate-containing material at atmospheric pressures and temperatures less than about 100 DEG F.
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Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation.
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