New insights into the mechanism governing the shear thinning effects observed in Nafion solutions, through the use of non-equilibrium, coarse-grained, molecular dynamic simulations.

From fine to coarse: insights into the large-scale assembly of poly(para-phenylene ethynylene)s from coarse-grained molecular dynamics simulations.

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The collective variables module (Colvars) is a software library that is tightly integrated with molecular simulation and analysis programs (Fiorin et al, Mol Phys, 2013). It is freely available in community programs for molecular dynamics such as NAMD and LAMMPS, and the visualization and analysis program VMD. Colvars implements reusable functions to reduce the dimensionality of complex chemical and biophysical systems, and a set of algorithms for enhanced sampling and statistical analysis. Recent updates have brought performance improvements for large systems and costly methods, a more flexible scripting interface, and the addition of more stable free energy estimators. We illustrate each advance through examples from biophysics, chemistry and materials science.