Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data.

ABSTRACT: The development of accurate implicit solvation models with low computational cost is essential for addressing many large-scale biophysical problems. Here, we present an efficient solvation term based on a Gaussian solvent-exclusion model (EEF1) for simulations of proteins in aqueous environment, with the primary aim of having a good overlap with explicit solvent simulations, particularly for unfolded and disordered states - as would be needed for multiscale applications. In order to achieve this, we have used a recently proposed coarse-graining procedure based on minimization of an entropy-related objective function to train the model to reproduce the equilibrium distribution obtained from explicit water simulations. Via this methodology, we have optimized both a charge screening parameter

SUBMITTER: Bottaro S 

PROVIDER: S-EPMC3987920 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature