Mixing Martinis: Hybrid Atomistic/Coarse-Grained Models for Protein Molecular Dynamics

Coarse-grained protein molecular dynamics simulations.

A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse grain...

ESPResSo 3.1: Molecular Dynamics Software for Coarse-Grained Models

ESPRESSO is a package for Molecular Dynamics (MD) simulations of coarse-grained models. We present the most recent version 3.1 of our software, highlighting some recent algorithmic extensions to version 1.0 presented in a previous paper (Limbach et al. Comput Phys Commun 174:704–727, 2006). A major strength of our package is the multitude of implemented methods for calculating Coulomb and dipol...

Coarse-grained molecular dynamics and continuum models for the transport of protein molecules

We describe protein transport across nanopores in a coarse-grained modeling. Numerical results reproduce a rich phenomenology, from fast transport to long blockades. Main translocation features are maintained in a 1D description of the process in an appropriate potential of the mean force. A second-rank tensor is selected as descriptor of the molecular shape. Its dynamics is identified by a pow...

Coarse Grained Molecular Dynamics

Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems

Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG) can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity....