Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications. The code and user guide can be downloaded at http://smog-server.org/smog2.

Experiments demonstrate that Mg2+ is crucial for structure and function of RNA systems, yet the detailed molecular mechanism of Mg2+ action on RNA is not well understood. We investigate the interplay between RNA and Mg2+ at atomic resolution through ten 2 microsecond explicit solvent molecular dynamics simulations of the SAM-I riboswitch with varying ion concentrations. The structure, including three stemloops, is very stable on this timescale. Simulations reveal that outer sphere coordinated Mg2+ ions fluctuate on the same time scale as the RNA, and that their dynamics couple. Locally, Mg2+ association affects RNA conformation through tertiary bridging interactions; globally, increasing Mg2+ concentration slows RNA fluctuations. Outer sphere Mg2+ ions responsible for these effects account for 80% of Mg2+ in our simulations. These ions are transiently bound to the RNA, maintaining interactions, but shuttled from site to site. Outer sphere Mg2+ are separated from the RNA by a single hydration shell, occupying a thin layer 3-5Å from the RNA. Distribution functions reveal outer sphere Mg2+ are positioned by electronegative atoms, hydration layers, and have a preference for the major groove. Diffusion analysis suggests transient outer sphere Mg2+ dynamics are glassy. Since outer sphere Mg2+ ions account for most of the Mg2+ in our simulations, these ions may change the paradigm of Mg2+-RNA interactions. Rather than a few inner sphere ions anchoring the RNA structure surrounded by a continuum of diffuse ions, we observe a layer of outer sphere coordinated Mg2+ that is transiently bound but strongly coupled to the RNA.

Multisite λ dynamics (MSλD) is a powerful emerging method in free energy calculation that allows prediction of relative free energies for a large set of compounds from very few simulations. Calculating free energy differences between substituents that constitute large volume or flexibility jumps in chemical space is difficult for free energy methods in general, and for MSλD in particular, due to large free energy barriers in alchemical space. This study demonstrates that a simple biasing potential can flatten these barriers and introduces an algorithm that determines system specific biasing potential coefficients. Two sources of error, deep traps at the endpoints and solvent disruption by hard-core potentials, are identified. Both scale with the size of the perturbed substituent and are removed by sharp biasing potentials and a new soft-core implementation, respectively. MSλD with landscape flattening is demonstrated on two sets of molecules: derivatives of the heat shock protein 90 inhibitor geldanamycin and derivatives of benzoquinone. In the benzoquinone system, landscape flattening leads to two orders of magnitude improvement in transition rates between substituents and robust solvation free energies. Landscape flattening opens up new applications for MSλD by enabling larger chemical perturbations to be sampled with improved precision and accuracy.