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JCC
2010
113views more  JCC 2010»
9 years 10 months ago
MDLab: A molecular dynamics simulation prototyping environment
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...
Trevor M. Cickovski, Santanu Chatterjee, Jacob Wen...
JCC
2002
81views more  JCC 2002»
9 years 11 months ago
Multiple grid methods for classical molecular dynamics
: 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...
Robert D. Skeel, Ismail Tezcan, David J. Hardy
PC
2000
105views Management» more  PC 2000»
9 years 11 months ago
New advances in chemistry and materials science with CPMD and parallel computing
A short overview is presented of the density functional theory and molecular dynamics (DFT
Wanda Andreoni, Alessandro Curioni
CPHYSICS
2004
89views more  CPHYSICS 2004»
9 years 11 months ago
Comprehensive suite of codes for plasma-edge modelling
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...
Ralf Schneider, Xavier Bonnin, Neil McTaggart, Ale...
BMCBI
2005
92views more  BMCBI 2005»
9 years 11 months ago
A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles
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...
Andreas Möglich, Daniel Weinfurtner, Till Mau...
BMCBI
2005
92views more  BMCBI 2005»
9 years 11 months ago
A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators
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...
Federico Fogolari, Silvio C. E. Tosatto, Giorgio C...
JCC
2008
84views more  JCC 2008»
9 years 11 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...
CPHYSICS
2006
95views more  CPHYSICS 2006»
9 years 11 months ago
Multibillion-atom molecular dynamics simulation: Design considerations for vector-parallel processing
Progress in adapting molecular dynamics algorithms for systems with short-range interactions to utilize the features of modern supercomputers is described. Efficient utilization o...
D. C. Rapaport
CPHYSICS
2008
161views more  CPHYSICS 2008»
9 years 11 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...
CORR
2008
Springer
77views Education» more  CORR 2008»
9 years 11 months ago
Programming an interpreter using molecular dynamics
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...
Jan A. Bergstra, C. A. Middelburg
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