Abstract
A new approach termed Adaptive Solvent-Scaling (AdSoS) is introduced for performing simulations of a solute embedded in a fine-grained (FG) solvent region itself surrounded by a coarse-grained (CG) solvent region, with a continuous FG ↔ CG switching of the solvent resolution across a buffer layer. Instead of relying on a distinct CG solvent model, the AdSoS scheme is based on CG models defined by a dimensional scaling of the FG solvent by a factor s, accompanied by an s-dependent modulation of the atomic masses and interaction parameters. The latter changes are designed to achieve an isomorphism between the dynamics of the FG and CG models, and to preserve the dispersive and dielectric solvation properties of the solvent with respect to a solute at FG resolution. This scaling approach offers a number of advantages compared to traditional coarse-graining: (i) the CG parameters are immediately related to those of the FG model (no need to parameterize a distinct CG model); (ii) nearly ideal mixing is expected for CG variants with similar s-values (ideal mixing holding in the limit of identical s-values); (iii) the solvent relaxation timescales should be preserved (no dynamical acceleration typical for coarse-graining); (iv) the graining level NG (number of FG molecules represented by one CG molecule) can be chosen arbitrarily (in particular, NG = s3 is not necessarily an integer); and (v) in an adaptive-resolution scheme, this level can be varied continuously as a function of the position (without requiring a bundling mechanism), and this variation occurs at a constant number of particles per molecule (no occurrence of fractional degrees of freedom in the buffer layer). By construction, the AdSoS scheme minimizes the thermodynamic mismatch between the different regions of the adaptive-resolution system, leading to a nearly homogeneous scaled solvent density s3ρ. Residual density artifacts in and at the surface of the boundary layer can easily be corrected by means of a grid-based biasing potential constructed in a preliminary pure-solvent simulation. This article introduces the AdSoS scheme and provides an initial application to pure atomic liquids (no solute) with Lennard-Jones plus Coulomb interactions in a slab geometry.
Highlights
Classical molecular dynamics (MD) simulations provide insight into the connection between microscopic interactions and macroscopic properties in the context ofmolecular systems, thereby explaining and complementing experimental observations
Instead of relying on a distinct CG solvent model, the Adaptive Solvent-Scaling (AdSoS) scheme is based on CG models defined by a dimensional scaling of the FG solvent by a factor s, accompanied by an s-dependent modulation of the atomic masses and interaction parameters
We propose a new adaptive-resolution scheme called Adaptive Solvent-Scaling (AdSoS), where the parameter s, which governs the scaling of the solvent, varies as a function of the position of a solvent molecule in space
Summary
Classical molecular dynamics (MD) simulations provide insight into the connection between microscopic interactions and macroscopic properties in the context of (bio)molecular systems, thereby explaining and complementing experimental observations. The influence of the implicit degrees of freedom on the explicit ones is handled by introducing corresponding mean-force (and, possibly, fluctuation) terms. Considering solvated (macro)molecules, one may distinguish two main approaches to reduce the number of degrees of freedom: implicit-solvent and coarse-grained models. In implicit-solvent scitation.org/journal/jcp models, the solvent is omitted and its influence on the solute degrees of freedom is represented by mean-force (non-polar and electrostatic) and fluctuation (stochastic and frictional) terms. In coarse-grained (CG) models, the resolution of the solute and/or solvent is reduced from individual atoms to beads representative of small groups of atoms, and the mean effect of the omitted intra-bead degrees of freedom is reintroduced by an appropriate parameterization of the effective potential energy function for interbead interactions. An early example of this approach is the use of united-atoms to represent the aliphatic CHn group as a single interaction site. United-atoms are often employed in models that are otherwise at fully atomistic resolution, and the word finegrained (FG) will be used here to denote models at (united-)atom resolution
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