Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition

Coarse Grained Molecular Dynamics

Elastic network models and coarse-grained NMA

The realization that experimentally observed functional motions of proteins can be predicted by coarse-grained normal mode analysis (NMA) has renewed interest in applications to structural biology. Notable applications include the prediction of biologically relevant motions for proteins and supramolecular structures driven by their structure-encoded collective dynamics; the refinement of low-re...

A Generic Force Field for Protein Coarse-Grained Molecular Dynamics Simulation

Coarse-grained (CG) force fields have become promising tools for studies of protein behavior, but the balance of speed and accuracy is still a challenge in the research of protein coarse graining methodology. In this work, 20 CG beads have been designed based on the structures of amino acid residues, with which an amino acid can be represented by one or two beads, and a CG solvent model with fi...

Iterative Force-Field Calculation and Molecular Dynamics of Cyclooctanone

Body's iterative force-field computer program has been used to calculate strain energies in cyclooctanone (I). 348 MHZ 1H NMR spectra of (I) have been investigated over the temperature range of 25° to -160°C. Two conformation processes affect the 1H NMR spectrum of (I). Iterative force-field calculations on the conformations and conformational interconversion paths of ...

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field.

It is widely recognized that atomistic Molecular Dynamics (MD), a classical simulation method, captures the essential physics of protein dynamics. That idea is supported by a theoretical study showing that various MD force-fields provide a consensus picture of protein fluctuations in aqueous solution [Rueda, M. et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796-801]. However, atomistic MD cann...