64,026 research outputs found
Adaptive multi-stage integrators for optimal energy conservation in molecular simulations
We introduce a new Adaptive Integration Approach (AIA) to be used in a wide
range of molecular simulations. Given a simulation problem and a step size, the
method automatically chooses the optimal scheme out of an available family of
numerical integrators. Although we focus on two-stage splitting integrators,
the idea may be used with more general families. In each instance, the
system-specific integrating scheme identified by our approach is optimal in the
sense that it provides the best conservation of energy for harmonic forces. The
AIA method has been implemented in the BCAM-modified GROMACS software package.
Numerical tests in molecular dynamics and hybrid Monte Carlo simulations of
constrained and unconstrained physical systems show that the method
successfully realises the fail-safe strategy. In all experiments, and for each
of the criteria employed, the AIA is at least as good as, and often
significantly outperforms the standard Verlet scheme, as well as fixed
parameter, optimized two-stage integrators. In particular, the sampling
efficiency found in simulations using the AIA is up to 5 times better than the
one achieved with other tested schemes
A Continuum,O(N) Monte-Carlo algorithm for charged particles
We introduce a Monte-Carlo algorithm for the simulation of charged particles
moving in the continuum. Electrostatic interactions are not instantaneous as in
conventional approaches, but are mediated by a constrained, diffusing electric
field on an interpolating lattice. We discuss the theoretical justifications of
the algorithm and show that it efficiently equilibrates model polyelectrolytes
and polar fluids. In order to reduce lattice artifacts that arise from the
interpolation of charges to the grid we implement a local, dynamic subtraction
algorithm. This dynamic scheme is completely general and can also be used with
other Coulomb codes, such as multigrid based methods
- …