Accurate Multiple Time Step in Biased Molecular Simulations

Accurate multiple time step in biased molecular simulations.

Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a bottleneck in molecular dynamics simulations. An algorithm to treat smooth biasing forces within a multiple time step framework is here discussed. The implementatio...

Multiple time step algorithms for molecular dynamics simulations of proteins: How good are they?

Ž . ABSTRACT: We evaluate several multiple time step MTS molecular Ž . dynamics MD methods with respect to their suitability for protein dynamics simulations. In contrast to the usual check of conservation of total energy or comparisons of trajectory details, we chose a problem-oriented approach and selected a set of relevant observables computed from extended test simulations. We define releva...

New Multiple Time-step Method for Molecular Dynamics Simulations of Nanocrystalline Materials

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins.Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show t...

Efficient multiple-time-step integrators with distance-based force splitting for particle-mesh-Ewald molecular dynamics simulations

We develop an efficient multiple-time-step force splitting scheme for particle-mesh-Ewald molecular dynamics simulations. Our method exploits smooth switch functions effectively to regulate direct and reciprocal space terms for the electrostatic interactions. The reciprocal term with the near field contributions removed is assigned to the slow class; the van der Waals and regulated particle-mes...