A Dynamic Time Step Method in Cytoskeletal Simulations

A Modified Multi Time Step Integration for Dynamic Analysis

In this paper new implicit higher order accuracy (N-IHOA) time integration based on assumption of constant time step is presented for dynamic analysis. This method belongs to the category of the multi time step integrations. Here, current displacement and velocity are assumed to be functions of the velocities and accelerations of several previous time steps, respectively. This definition causes...

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...

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

S-Step BiCGStab Algorithms for Geoscience Dynamic Simulations

In basin and reservoir simulations, the most expensive and time consuming phase is solving systems of linear equations using Krylov subspace methods such as BiCGStab. For this reason, we explore the possibility of using communication avoiding Krylov subspace methods (s-step BiCGStab), that speedup of the convergence time on modern-day architectures, by restructuring the algorithms to reduce com...

Multicanonical Simulations Step by Step

The purpose of this article is to provide a starter kit for multicanonical simulations in statistical physics. Fortran code for the q-state Potts model in d = 2, 3, . . . dimensions can be downloaded from the Web and this paper describes simulation results, which are in all details reproducible by running prepared programs. To allow for comparison with exact results, the internal energy, the sp...