JCC
2010
13 years 3 months ago
2010
Molecular dynamics (MD) simulation involves solving Newton’s equations of motion for a system of atoms, by calculating forces and updating atomic positions and velocities over a...
JCC
2002
13 years 4 months ago
2002
: Presented in the context of classical molecular mechanics and dynamics are multilevel summation methods for the fast calculation of energies/forces for pairwise interactions, whi...
PC
2000
13 years 4 months ago
2000
A short overview is presented of the density functional theory and molecular dynamics (DFT
CPHYSICS
2004
13 years 4 months ago
2004
The various aspects of plasma-edge physics are included in a comprehensive suite of codes having applications from industrial plasmas to fusion devices. Here the basic ideas, stat...
BMCBI
2005
13 years 4 months ago
2005
Background: We have developed the program PERMOL for semi-automated homology modeling of proteins. It is based on restrained molecular dynamics using a simulated annealing protoco...
BMCBI
2005
13 years 4 months ago
2005
Background: Estimators of free energies are routinely used to judge the quality of protein structural models. As these estimators still present inaccuracies, they are frequently e...
JCC
2008
13 years 4 months ago
2008
: 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...
CPHYSICS
2006
13 years 4 months ago
2006
Progress in adapting molecular dynamics algorithms for systems with short-range interactions to utilize the features of modern supercomputers is described. Efficient utilization o...
CPHYSICS
2008
13 years 4 months ago
2008
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 ...
CORR
2008
Springer
13 years 4 months ago
2008
Springer
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation deve...