Comparing molecular dynamics force fields in the essential subspace.

ABSTRACT: The continued development and utility of molecular dynamics simulations requires improvements in both the physical models used (force fields) and in our ability to sample the Boltzmann distribution of these models. Recent developments in both areas have made available multi-microsecond simulations of two proteins, ubiquitin and Protein G, using a number of different force fields. Although these force fields mostly share a common mathematical form, they differ in their parameters and in the philosophy by which these were derived, and previous analyses showed varying levels of agreement with experimental NMR data. To complement the comparison to experiments, we have performed a structural analysis of and comparison between these simulations, thereby providing insight into the relationship be

SUBMITTER: Martin-Garcia F 

PROVIDER: S-EPMC4374674 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature