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JCC
2008
84views more  JCC 2008»
13 years 8 months ago
Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules
: An explicit ion, implicit water solvent model for molecular dynamics was developed and tested with DNA and RNA simulations. The implicit water model uses the finite difference Po...
Ninad V. Prabhu, Manoranjan Panda, Qingyi Yang, Ki...
ICCS
2004
Springer
14 years 1 months ago
A Tool Suite for Simulation Based Analysis of Memory Access Behavior
In this paper, two tools are presented: an execution driven cache simulator which relates event metrics to a dynamically built-up call-graph, and a graphical front end able to visu...
Josef Weidendorfer, Markus Kowarschik, Carsten Tri...
CPHYSICS
2008
161views more  CPHYSICS 2008»
13 years 8 months ago
Implementing peridynamics within a molecular dynamics code
Peridynamics (PD) is a continuum theory that employs a nonlocal model to describe material properties. In this context, nonlocal means that continuum points separated by a finite ...
Michael L. Parks, Richard B. Lehoucq, Steven J. Pl...
ICA3PP
2005
Springer
14 years 1 months ago
GridMD: Program Architecture for Distributed Molecular Simulation
In the present work we describe architectural concepts of the distributed molecular simulation package GridMD. The main purpose of this work is to underline the construction patter...
Ilya Valuev
ICCS
2001
Springer
14 years 11 days ago
Supporting Car-Parrinello Molecular Dynamics with UNICORE
This paper presents the integration of application specific interfaces in the UNICORE Grid infrastructure. UNICORE provides a seamless and secure mechanism to access distributed s...
Valentina Huber