Add to ORKGAn algorithm is presented for running SHAKE in parallel. SHAKE is a widely used approach to compute molecular dynamics trajectories with constraints. An essential step in SHAKE is the solution of a sparse linear problem of the type Ax b = where x is a vector of unknowns. Conjugate gradient minimization (that can be done in parallel) replaces the widely used iteration process that is inherently serial. Numerical examples present good load balancing and are limited only by communication time
summary:In the first part of the paper we survey some algorithms which describe time evolution of in...
Methods for performing large-scale parallel Molecular Dynamics(MD) simulations are investigated. A ...
In this paper we consider a new class of search and optimization algorithms inspired by molecular d...
SHAKE is a widely used algorithm to impose general holonomic constraints during molecular simulation...
An algorithm, called RATTLE, for integrating the equations of motion in molecular dynamics calculati...
This paper describes the techniques and methodologies employed during parallelization of the Molecul...
SHAKE and RATTLE algorithms are widely used in molecular dynamics simulations and for this reason ar...
We describe a method to impose constraints in a molecular dynamics simulation. A technique developed...
Molecular dynamics is used to study the time evolution of systems of atoms. It is common to constrai...
Published under license in Journal of Physics: Conference Series.Recently, an alternative strategy f...
The performance of some algorithms, running on a message passing computer; is limited by the high la...
In molecular dynamics simulations we can often increase the time step by imposing constraints on bon...
Molecular dynamics is used to study the time evolution of systems of atoms. It is common to constrai...
Molecular dynamics simulation is a well-established technique for modeling complex many-particle sys...
. This report describes a parallelization of the University of Houston Brownian Dynamics (UHBD) prog...
summary:In the first part of the paper we survey some algorithms which describe time evolution of in...
Methods for performing large-scale parallel Molecular Dynamics(MD) simulations are investigated. A ...
In this paper we consider a new class of search and optimization algorithms inspired by molecular d...
SHAKE is a widely used algorithm to impose general holonomic constraints during molecular simulation...
An algorithm, called RATTLE, for integrating the equations of motion in molecular dynamics calculati...
This paper describes the techniques and methodologies employed during parallelization of the Molecul...
SHAKE and RATTLE algorithms are widely used in molecular dynamics simulations and for this reason ar...
We describe a method to impose constraints in a molecular dynamics simulation. A technique developed...
Molecular dynamics is used to study the time evolution of systems of atoms. It is common to constrai...
Published under license in Journal of Physics: Conference Series.Recently, an alternative strategy f...
The performance of some algorithms, running on a message passing computer; is limited by the high la...
In molecular dynamics simulations we can often increase the time step by imposing constraints on bon...
Molecular dynamics is used to study the time evolution of systems of atoms. It is common to constrai...
Molecular dynamics simulation is a well-established technique for modeling complex many-particle sys...
. This report describes a parallelization of the University of Houston Brownian Dynamics (UHBD) prog...
summary:In the first part of the paper we survey some algorithms which describe time evolution of in...
Methods for performing large-scale parallel Molecular Dynamics(MD) simulations are investigated. A ...
In this paper we consider a new class of search and optimization algorithms inspired by molecular d...