Multiscale Simulation of Liquid Water Using a Four-to-One Mapping for Coarse-Graining

Predictive scale-bridging simulations through active learning

Throughout computational science, there is a growing need to utilize the continual improvements in raw computational horsepower to achieve greater physical fidelity through scale-bridging over brute-force increases in the number of mesh elements. For instance, quantitative predictions of transport in nanoporous media, critical to hydrocarbon extraction from tight shale formations, are impossible without accounting for molecular-level interactions. Similarly, inertial confinement fusion simulations rely on numerical diffusion to simulate molecular effects such as non-local transport and mixing without truly accounting for molecular interactions. With these two disparate applications in mind, we develop a novel capability which uses an active learning approach to optimize the use of local fine-scale simulations for informing coarse-scale hydrodynamics. Our approach addresses three challenges: forecasting continuum coarse-scale trajectory to speculatively execute new fine-scale molecular dynamics calculations, dynamically updating coarse-scale from fine-scale calculations, and quantifying uncertainty in neural network models.

Multiscale Simulation of Protein Hydration Using the SWINGER Dynamical Clustering Algorithm

To perform computationally efficient concurrent multiscale simulations of biological macromolecules in solution, where the all-atom (AT) models are coupled to supramolecular coarse-grained (SCG) solvent models, previous studies resorted to modified AT water models, such as the bundled-simple point charge (SPC) models, that use semiharmonic springs to restrict the relative movement of water molecules within a cluster. Those models can have a significant impact on the simulated biomolecules and can lead, for example, to a partial unfolding of a protein. In this work, we employ the recently developed alternative approach with a dynamical clustering algorithm, SWINGER, which enables a direct coupling of original unmodified AT and SCG water models. We perform an adaptive resolution molecular dynamics simulation of a Trp-Cage miniprotein in multiscale water, where the standard SPC water model is interfaced with the widely used MARTINI SCG model, and demonstrate that, compared to the corresponding full-blown AT simulations, the structural and dynamic properties of the solvated protein and surrounding solvent are well reproduced by our approach.

Adaptive resolution simulations of biomolecular systems

In this review article, we discuss and analyze some recently developed hybrid atomistic-mesoscopic solvent models for multiscale biomolecular simulations. We focus on the biomolecular applications of the adaptive resolution scheme (AdResS), which allows solvent molecules to change their resolution back and forth between atomistic and coarse-grained representations according to their positions in the system. First, we discuss coupling of atomistic and coarse-grained models of salt solution using a 1-to-1 molecular mapping-i.e., one coarse-grained bead represents one water molecule-for development of a multiscale salt solution model. In order to make use of coarse-grained molecular models that are compatible with the MARTINI force field, one has to resort to a supramolecular mapping, in particular to a 4-to-1 mapping, where four water molecules are represented with one coarse-grained bead. To this end, bundled atomistic water models are employed, i.e., the relative movement of water molecules that are mapped to the same coarse-grained bead is restricted by employing harmonic springs. Supramolecular coupling has recently also been extended to polarizable coarse-grained water models with explicit charges. Since these coarse-grained models consist of several interaction sites, orientational degrees of freedom of the atomistic and coarse-grained representations are coupled via a harmonic energy penalty term. The latter aligns the dipole moments of both representations. The reviewed multiscale solvent models are ready to be used in biomolecular simulations, as illustrated in a few examples.

Adaptive resolution simulation of oligonucleotides

Nucleic acids are characterized by a complex hierarchical structure and a variety of interaction mechanisms with other molecules. These features suggest the need of multiscale simulation methods in order to grasp the relevant physical properties of deoxyribonucleic acid (DNA) and RNA using in silico experiments. Here we report an implementation of a dual-resolution modeling of a DNA oligonucleotide in physiological conditions; in the presented setup only the nucleotide molecule and the solvent and ions in its proximity are described at the atomistic level; in contrast, the water molecules and ions far from the DNA are represented as computationally less expensive coarse-grained particles. Through the analysis of several structural and dynamical parameters, we show that this setup reliably reproduces the physical properties of the DNA molecule as observed in reference atomistic simulations. These results represent a first step towards a realistic multiscale modeling of nucleic acids and provide a quantitatively solid ground for their simulation using dual-resolution methods.

Adaptive Resolution Simulation of Supramolecular Water: The Concurrent Making, Breaking, and Remaking of Water Bundles

The adaptive resolution scheme (AdResS) is a multiscale molecular dynamics simulation approach that can concurrently couple atomistic (AT) and coarse-grained (CG) resolution regions, i.e., the molecules can freely adapt their resolution according to their current position in the system. Coupling to supramolecular CG models, where several molecules are represented as a single CG bead, is challenging, but it provides higher computational gains and connection to the established MARTINI CG force field. Difficulties that arise from such coupling have been so far bypassed with bundled AT water models, where additional harmonic bonds between oxygen atoms within a given supramolecular water bundle are introduced. While these models simplify the supramolecular coupling, they also cause in certain situations spurious artifacts, such as partial unfolding of biomolecules. In this work, we present a new clustering algorithm SWINGER that can concurrently make, break, and remake water bundles and in conjunction with the AdResS permits the use of original AT water models. We apply our approach to simulate a hybrid SPC/MARTINI water system and show that the essential properties of water are correctly reproduced with respect to the standard monoscale simulations. The developed hybrid water model can be used in biomolecular simulations, where a significant speed up can be obtained without compromising the accuracy of the AT water model.

Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA

We discuss recent advances of the VOTCA package for systematic coarse-graining. Two methods have been implemented, namely the downhill simplex optimization and the relative entropy minimization. We illustrate the new methods by coarse-graining SPC/E bulk water and more complex water-methanol mixture systems. The CG potentials obtained from both methods are then evaluated by comparing the pair distributions from the coarse-grained to the reference atomistic simulations. In addition to the newly implemented methods, we have also added a parallel analysis framework to improve the computational efficiency of the coarse-graining process.

Systematic evaluation of bundled SPC water for biomolecular simulations

How accurate is bundled SPC water as inner shell solvent for hybrid all-atom/coarse-grained simulations?

Direct Mixing of Atomistic Solutes and Coarse-Grained Water

We present a new dual-resolution approach for coupling atomistic and coarse-grained models in molecular dynamics simulations of hydrated systems. In particular, a coarse-grained point dipolar water model is used to solvate molecules represented with standard all-atom force fields. A unique characteristic of our methodology is that the mixing of resolutions is direct, meaning that no additional or ad hoc scaling factors, intermediate regions, or extra sites are required. To validate the methodology, we compute the hydration free energy of 14 atomistic small molecules (analogs of amino acid side chains) solvated by the coarse-grained water. Remarkably, our predictions reproduce the experimental data as accurately as the predictions from state-of-the-art fully atomistic simulations. We also show that the hydration free energy of the coarse-grained water itself is in comparable or better agreement with the experimental value than the predictions from all but one of the most common multisite atomistic models. The coarse-grained water is then applied to solvate a typical atomistic protein containing both α-helix and β-strand elements. Moreover, parallel tempering simulations are performed to investigate the folding free energy landscape of a representative α helical and a β hairpin structure. For the simulations considered in this work, our dual-resolution method is found to be 3 to 6 times more computationally efficient than corresponding fully atomistic approaches.

Combining the Fluctuating Charge Method, Non-Periodic Boundary Conditions and Meta-Dynamics: Aqua Ions as case studies

We present the current status of development of our code for performing Molecular Dynamics (MD) simulations exploiting a polarizable force field based on the Fluctuating Charge (FQ) method and non-Periodic Boundary Conditions (NPBC). Continuing on the path set in a previous work, we increased the capabilities of the code by implementing a number of new features, including: a non-iterative algorithm for rigid trigonal molecule simulations; two additional temperature coupling schemes; a meta-dynamics based approach for effective free energy evaluations. Although these are well known algorithms, each present in one or more widely used MD packages, they have now been tested, for the first time, in the context of the FQ model coupled with NPBC. As case studies, we considered three aqueous ions of increasing charge, namely Na⁺, Ca²⁺ and La³⁺, at infinite dilution. In particular, by exploiting a computational approach recently proposed by our group and based on the metadynamics technique, we focused on the important role played by solvent polarization on ionic hydration structures, also investigating the free energy landscapes of ion coordination and the water exchange rates. Such an approach, previously tested with standard non-polarizable models, was applied here to evaluate the effects of explicit polarization on water exchange barriers between different solvent coordination structures. Moreover, we have analyzed and discussed in some detail non-linear electrostatic effects arising from solvent polarization while going from a mono- to a di- and trivalent ion.