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Register a new userAccurate Thermodynamics for Short-Ranged Truncations of Coulomb Interactions in Site-Site Molecular Models
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Coulomb interactions are present in a wide variety of all-atom force fields. Spherical truncations of these interactions permit fast simulations but are problematic due to their incorrect thermodynamics. Herein we demonstrate that simple analytical corrections for the thermodynamics of uniform truncated systems are possible. In particular results for the SPC/E water model treated with spherically-truncated Coulomb interactions suggested by local molecular field theory [Proc. Nat. Acad. Sci. USA 105, 19136 (2008)] are presented. We extend results developed by Chandler [J. Chem. Phys. 65, 2925 (1976)] so that we may treat the thermodynamics of mixtures of flexible charged and uncharged molecules simulated with spherical truncations. We show that the energy and pressure of spherically-truncated bulk SPC/E water are easily corrected using exact second-moment-like conditions on long-ranged structure. Furthermore, applying the pressure correction as an external pressure removes the density errors observed by other research groups in NPT simulations of spherically-truncated bulk species.
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We show that spherical truncations of the 1/r interactions in models for water and acetonitrile yield very accurate results in bulk simulations for all site-site pair correlation functions as well as dipole-dipole correlation functions. This good performance in bulk simulations contrasts with the generally poor results found with the use of such truncations in nonuniform molecular systems. We argue that Local Molecular Field (LMF) theory provides a general theoretical framework that gives the necessary corrections to simple truncations in most nonuniform environments and explains the accuracy of spherical truncations in uniform environments by showing that these corrections are very small. LMF theory is derived from the exact Yvon-Born-Green (YBG) hierarchy by making physically-motivated and well-founded approximations. New and technically interesting derivations of both the YBG hierarchy and LMF theory for a variety of site-site molecular models are presented in appendices. The main paper focuses on understanding the accuracy of these spherical truncations in uniform systems both phenomenologically and quantitatively using LMF theory.
We extend results developed by Chandler [J. Chem. Phys. 65, 2925 (1976)] for the dielectric constant of neutral site-site molecular models to mixtures of both charged and uncharged molecules. This provides a unified derivation connecting the Stillinger-Lovett moment conditions for ions to standard results for the dielectric constant for polar species and yields exact expressions for the small-k expansion of the two-point intermolecular charge-density function used to determine the total Coulomb energy. The latter is useful in determining corrections to the thermodynamics of uniform site-site molecular models simulated with spherically truncated Coulomb interactions.
In our first paper, we showed how a non-local effective Hamiltionian for short-ranged wetting may be derived from an underlying Landau-Ginzburg-Wilson model. Here, we combine the Greens function method with standard perturbation theory to determine the general diagrammatic form of the binding potential functional beyond the double-parabola approximation for the Landau-Ginzburg-Wilson bulk potential. The main influence of cubic and quartic interactions is simply to alter the coefficients of the double parabola-like zig-zag diagrams and also to introduce curvature and tube-interaction corrections (also represented diagrammatically), which are of minor importance. Non-locality generates effective long-ranged many-body interfacial interactions due to the reflection of tube-like fluctuations from the wall. Alternative wall boundary conditions (with a surface field and enhancement) and the diagrammatic description of tricritical wetting are also discussed.
We propose a simplified version of local molecular field (LMF) theory to treat Coulomb interactions in simulations of ionic fluids. LMF theory relies on splitting the Coulomb potential into a short-ranged part that combines with other short-ranged core interactions and is simulated explicitly. The averaged effects of the remaining long-ranged part are taken into account through a self-consistently determined effective external field. The theory contains an adjustable length parameter sigma that specifies the cut-off distance for the short-ranged interaction. This can be chosen to minimize the errors resulting from the mean-field treatment of the complementary long-ranged part. Here we suggest that in many cases an accurate approximation to the effective field can be obtained directly from the equilibrium charge density given by the Debye theory of screening, thus eliminating the need for a self-consistent treatment. In the limit sigma -> 0, this assumption reduces to the classical Debye approximation. We examine the numerical performance of this approximation for a simple model of a symmetric ionic mixture. Our results for thermodynamic and structural properties of uniform ionic mixtures agree well with similar results of Ewald simulations of the full ionic system. In addition we have used the simplified theory in a grand-canonical simulation of a nonuniform ionic mixture where an ion has been fixed at the origin. Simulations using short-ranged truncations of the Coulomb interactions alone do not satisfy the exact condition of complete screening of the fixed ion, but this condition is recovered when the effective field is taken into account. We argue that this simplified approach can also be used in the simulations of more complex nonuniform systems.
Current all-atom potential based molecular dynamics (MD) allow the identification of a proteins functional motions on a wide-range of time-scales, up to few tens of ns. However, functional large scale motions of proteins may occur on a time-scale currently not accessible by all-atom potential based molecular dynamics. To avoid the massive computational effort required by this approach several simplified schemes have been introduced. One of the most satisfactory is the Gaussian Network approach based on the energy expansion in terms of the deviation of the protein backbone from its native configuration. Here we consider an extension of this model which captures in a more realistic way the distribution of native interactions due to the introduction of effective sidechain centroids. Since their location is entirely determined by the protein backbone, the model is amenable to the same exact and computationally efficient treatment as previous simpler models. The ability of the model to describe the correlated motion of protein residues in thermodynamic equilibrium is established through a series of successful comparisons with an extensive (14 ns) MD simulation based on the AMBER potential of HIV-1 protease in complex with a peptide substrate. Thus, the model presented here emerges as a powerful tool to provide preliminary, fast yet accurate characterizations of proteins near-native motion.
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