All calculated DeltaG values were based on molecular dynamics simulations with explicit solvent.

Finally, we present results of molecular dynamics simulations in explicit solvent to confirm our conclusions.

The presented PB radii were optimized using results from explicit solvent simulations of the large systems.

Inclusion of a second shell of explicit solvent was found to be unnecessary for these peptides.

We report over 30 μs of unrestrained molecular dynamics simulations of six protein-RNA complexes in explicit solvent.

Ensembles obtained from hybrid REMD are in very close agreement with explicit solvent data, predominantly populating polyproline II conformations.

Modern atomic resolution, explicit solvent molecular dynamics simulations have contributed to our understanding of DNA fine structure and conformational polymorphism.

Also, in explicit solvent molecular dynamics simulations, protein G B1 maintained its predicted orientation in three out of four runs.

Likewise, using only the solvation shells and no continuum model resulted in ensembles that differed significantly from the standard explicit solvent data.

The detailed hydration of the two disaccharides was described using three force fields especially developed for modeling of carbohydrates in explicit solvent.

While explicit solvent representations result in highly accurate models, they also require extensive sampling due to the high number of solvent degrees of freedom.

In the present study, we complement the experiments by free energy computations using thermodynamics integration method based on extended explicit solvent molecular dynamics simulations.

We here present new PB radii for the AMBER protein force field to accurately reproduce the solvation free energies obtained from explicit solvent simulations.

We examine the dynamical (un)folding pathways of the C-terminal beta-hairpin of protein G-B1 at room temperature in explicit solvent, by employing transition path sampling algorithms.

Explicit solvent molecular dynamics simulations have been used to complement preceding experimental and computational studies of folding of guanine quadruplexes (G-DNA).