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BMCBI
2011
10 years 8 months ago
Implementation of Force Distribution Analysis for Molecular Dynamics simulations
Background: The way mechanical stress is distributed inside and propagated by proteins and other biopolymers largely defines their function. Yet, determining the network of intera...
Wolfram Stacklies, Christian Seifert, Frauke Graet...
JCPHY
2011
192views more  JCPHY 2011»
10 years 4 months ago
Fast analysis of molecular dynamics trajectories with graphics processing units - Radial distribution function histogramming
The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in ...
Benjamin G. Levine, John E. Stone, Axel Kohlmeyer
JCC
2002
94views more  JCC 2002»
11 years 1 months ago
Modern protein force fields behave comparably in molecular dynamics simulations
: Several molecular dynamics simulations were performed on three proteins--bovine apo-calbindin D9K, human interleukin-4 R88Q mutant, and domain IIA of bacillus subtilis glucose pe...
Daniel J. Price, Charles L. Brooks III
CPHYSICS
2008
121views more  CPHYSICS 2008»
11 years 1 months ago
A scalable parallel algorithm for large-scale reactive force-field molecular dynamics simulations
A scalable parallel algorithm has been designed to perform multimillion-atom molecular dynamics (MD) simulations, in which first principlesbased reactive force fields (ReaxFF) des...
Ken-ichi Nomura, Rajiv K. Kalia, Aiichiro Nakano, ...
APVIS
2011
10 years 1 months ago
Loose capacity-constrained representatives for the qualitative visual analysis in molecular dynamics
Molecular dynamics is a widely used simulation technique to investigate material properties and structural changes under external forces. The availability of more powerful cluster...
Steffen Frey, Thomas Schlömer, Sebastian Grot...
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