DNA-protamine condensates under low salt conditions: Molecular dynamics simulation with a simple coarse-grained model focusing on electrostatic interactions

IBIsCO: A molecular dynamics simulation package for coarse-grained simulation

IBIsCO is a parallel molecular dynamics simulation package developed specially for coarse-grained simulations with numerical potentials derived by the iterative Boltzmann inversion (IBI) method (Reith et al., J Comput Chem 2003, 24, 1624). In addition to common features of molecular dynamics programs, the techniques of dissipative particle dynamics (Groot and Warren, J Chem Phys 1997, 107, 4423...

Coarse Grained Molecular Dynamics

A Coarse-Grained DNA Model for Bubble Formation and Dynamics

A coarse-grained molecular dynamics model for crystalline solids

A general mathematical framework for coarse-graining molecular dynamics (MD) model for solid system is presented. The formulation is based directly on the full MD model. The reduction of the atomic degrees of freedom is accomplished using the Mori–Zwanzig projection method. We also demonstrate how to simplify the model under this framework to make the numerical implementation much easier. Copyr...

A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations.

The development of coarse-grained (CG) models that correctly represent the important features of compounds is essential to overcome the limitations in time scale and system size currently encountered in atomistic molecular dynamics simulations. Most approaches reported in the literature model one or several molecules into a single uncharged CG bead. For water, this implicit treatment of the ele...