Gregory A. Voth

Flexible simple point-charge water model with improved liquid-state properties

In order to introduce flexibility into the simple point-charge (SPC) water model, the impact of the intramolecular degrees of freedom on liquid properties was systematically studied in this work as a function of many possible parameter sets. It was found that the diffusion constant is extremely sensitive to the equilibrium bond length and that this effect is mainly due to the strength of intermolecular hydrogen bonds. The static dielectric constant was found to be very sensitive to the equilibrium bond angle via the distribution of intermolecular angles in the liquid: A larger bond angle will increase the angle formed by two molecular dipoles, which is particularly significant for the first solvation shell. This result is in agreement with the work of Hochtl et al. [J. Chem. Phys. 109, 4927 (1998)]. A new flexible simple point-charge water model was derived by optimizing bulk diffusion and dielectric constants to the experimental values via the equilibrium bond length and angle. Due to the large sensitivities, the parametrization only slightly perturbs the molecular geometry of the base SPC model. Extensive comparisons of thermodynamic, structural, and kinetic properties indicate that the new model is much improved over the standard SPC model and its overall performance is comparable to or even better than the extended SPC model.

THE COMPUTER SIMULATION OF PROTON TRANSPORT IN WATER

The dynamics and energetics of an excess proton in bulk phase water are examined computationally with a special emphasis on a quantum-dynamical treatment of the nuclear motion. The potential model used, the recently developed multistate empirical valence bond (MS-EVB) approach [U. W. Schmitt and G. A. Voth, J. Phys. Chem. B 102, 5547 (1998)], is also further refined and described in more detail. The MS-EVB model takes into account the interaction of an exchange charge distribution of the charge-transfer complex with the polar solvent, which qualitatively changes the nature of the solvated complex. Classical and quantum molecular dynamics simulations of the excess proton in bulk phase water reveal that quantization of the nuclear degrees of freedom results in an increased stabilization of the solvated H5O2+ (Zundel) cation relative to the H9O4+ (Eigen) cation, though the latter is still more stable, and that a species intermediate between the two also exists. The quantum proton transport rate, which is eva...

Rigorous formulation of quantum transition state theory and its dynamical corrections

We describe a procedure for computing the thermal rate constants for infrequent events that occur in complicated quantum mechanical systems. Following the ideas of Gillan, the procedure focuses on the equilibrium statistics of the centroids for the imaginary time quantum paths. We argue that the imaginary time statistics can be used to efficiently bias Monte Carlo sampling of the real time reaction dynamics. Consideration of imaginary time paths or equilibrium statistics alone leads to a quantum transition state theory. Analytical versions of this transition state theory are developed with the aid of a variational principle. Numerical applications of the quantum transition state theory are given for the one‐dimensional Eckart barrier problem and for the nonseparable two‐dimensional collinear H2+H reaction. Remarkably accurate results are obtained. The quantum transition state theory we describe provides a rigorous basis and generalizes algorithms recently employed to treat electron transfer and also ioniz...

Multiscale coarse graining of liquid-state systems

A methodology is described to systematically derive coarse-grained (CG) force fields for molecular liquids from the underlying atomistic-scale forces. The coarse graining of an interparticle force field is accomplished by the application of a force-matching method to the trajectories and forces obtained from the atomistic trajectory and force data for the CG sites of the targeted system. The CG sites can be associated with the centers of mass of atomic groups because of the simplicity in the evaluation of forces acting on these sites from the atomistic data. The resulting system is called a multiscale coarse-grained (MS-CG) representation. The MS-CG method for liquids is applied here to water and methanol. For both liquids one-site and two-site CG representations without an explicit treatment of the long-ranged electrostatics have been derived. In addition, for water a two-site model having the explicit long-ranged electrostatics has been developed. To improve the thermodynamic properties (e.g., pressure and density) for the MS-CG models, the constraint for the instantaneous virial was included into the force-match procedure. The performance of the resulting models was evaluated against the underlying atomistic simulations and experiment. In contrast with existing approaches for coarse graining of liquid systems, the MS-CG approach is general, relies only on the interatomic interactions in the reference atomistic system.

The formulation of quantum statistical mechanics based on the Feynman path centroid density. II. Dynamical properties

The formulation of quantum dynamical time correlation functions is examined within the context of the path centroid variable in Feynman path integration. This study builds on the centroid‐based approach to equilibrium properties developed in the companion paper. The introduction of the centroid perspective into the calculation of real time position correlation functions is outlined and an intriguing quasiclassical role for the centroid variable in real time position correlation functions is identified. This quasiclassical perspective is developed in terms of general interaction potentials, and the computational effort in implementing the method should scale with the size of the system in the same fashion as a classical molecular dynamics calculation. The centroid‐based theory is also implemented in several different approaches to calculate general time correlation functions. The theoretical results are illustrated and tested by representative numerical applications.

Coarse-graining of condensed phase and biomolecular systems

Introduction Gregory A. Voth The MARTINI Force Field Siewert J. Marrink, Marc Fuhrmans, H. Jelger Risselada, and Xavier Periole The Multiscale Coarse-Graining Method: A Systematic Approach to Coarse Graining W.G. Noid, Gary S. Ayton, Sergei Izvekov, and Gregory A. Voth A Model for Lipid Bilayers in Implicit Solvent Grace Brannigan, and Frank L.H. Brown Coarse-Grained Dynamics of Anisotropic Systems L. Paramonov, M.G. Burke, and S.N. Yaliraki State-Point Dependence and Transferability of Potentials in Systematic Structural Coarse-Graining Qi Sun, Jayeeta Ghosh, and Roland Faller Systematic Approach to Coarse-Graining of Molecular Descriptions and Interactions with Applications to Lipid Membranes Teema Murtola, Ilpo Vattulainen, and Mikko Karttunen Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field Adam Liwo, Cezary Czaplewski, Stanislaw Oldziej, Ana V. Rojas, Rajmund Kazmierkiewicz, Mariusz Makowski, Rajesh K. Murarka, and Harold A. Scheraga Coarse-Grained Structure-Based Simulations of Proteins and RNA Alexander Schug, Changbong Hyeon, and Jose N. Onuchic On the Development of Coarse-Grained Protein Models: Importance of Relative Side-Chain Orientations and Backbone Interactions N.-V. Buchete, J.E. Straub, and D. Thirumalai Characterization of Protein-Folding Landscapes by Coarse-Grain Models Incorporating Experimental Data Silvina Matysiak and Cecilia Clementi Principles and Practicalities of Canonical Mixed-Resolution Sampling of Biomolecules Daniel M. Zuckerman Pathways of Conformational Transitions in Proteins Peter Majek, Ron Elber, and Harel Weinstein Insights into the Sequence-Dependent Macromolecular Properties of DNA from Base-Pair Level Modeling Wilma K. Olson, Andrew V. Colasanti, Luke Czapla, and Guohui Zheng Coarse-Grain Models for Nucleic Acids and Large Nucleoprotein Assemblies Robert K.-Z. Tan, Anton S. Petrov, Batsal Devkota, and Stephen C. Harvey Elastic Network Models of Coarse-Grained Proteins Are Effective for Studying the Structural Control Exerted over Their Dynamics Robert L. Jernigan, Lei Yang, Ozge Kurkcuoglu, Guang Song, and Pemra Doruker Coarse-Grained Elastic Normal Mode Analysis and Its Applications in X-Ray Crystallographic Refinement at Moderate Resolutions Jianpeng Ma Coarse-Grained Normal Mode Analysis to Explore Large-Scale Dynamics of Biological Molecules Osamu Miyashita and Florence Tama One-Bead Coarse-Grained Models for Proteins Valentina Tozzini and J. Andrew McCammon Application of Residue-Based and Shape-Based Coarse-Graining to Biomolecular Simulations Peter L. Freddolino, Anton Arkhipov, Amy Y. Shih, Ying Ying, Zhongzhou Chen, and Klaus Schulten Coarse-Graining Protein Mechanics Richard Lavery and Sophie Sacquin-Mora Self-Assembly of Surfactants in Bulk Phases and at Interfaces Using Coarse-Grain Models Wataru Shindoa, Russell DeVane, and Michael L. Klein Coarse-Grained Simulations of Polyelectrolytes Mark J. Stevens Monte Carlo Simulations of a Coarse-Grain Model for Block Copolymer Systems F.A. Detcheverry, K.Ch. Daoulas, P.F. Nealey, M. Muller, and J.J. de Pablo Structure-Based Coarse- and Fine-Graining in Soft Matter Simulations Nico F.A. van der Vegt, Christine Peter, and Kurt Kremer From Atomistic Modeling of Macromolecules toward Equations of State for Polymer Solutions and Melts: How Important Is the Accurate Description of the Local Structure? Kurt Binder, Wolfgang Paul, Peter Virnau, Leonid Yelash, Marcus Muller, and Luis Gonzalez MacDowell Effective Interaction Potentials for Coarse-Grained Simulations of Polymer-Tethered Nanoparticle Self-Assembly in Solution Elaine R. Chan, Alberto Striolo, Clare McCabe, Peter T. Cummings, and Sharon C. Glotzer Coarse-Graining in Time: From Microscopics to Macroscopics Angela Violi Index

Ab initio molecular dynamics: Propagating the density matrix with Gaussian orbitals

We propose and implement an alternative approach to the original Car–Parrinello method where the density matrix elements (instead of the molecular orbitals) are propagated together with the nuclear degrees of freedom. Our new approach has the advantage of leading to an O(N) computational scheme in the large system limit. Our implementation is based on atom-centered Gaussian orbitals, which are especially suited to deal effectively with general molecular systems. The methodology is illustrated by applications to the three-body dissociation of triazine and to the dynamics of a cluster of a chloride ion with 25 water molecules.

Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: A new method for force-matching

A novel least-squares fitting approach is presented to obtain classical force fields from trajectory and force databases produced by ab initio (e.g., Car-Parrinello) molecular dynamics (MD) simulations. The method was applied to derive effective nonpolarizable three-site force fields for liquid water at ambient conditions from Car-Parrinello MD simulations in the Becke-Lee-Yang-Parr approximation to the electronic density functional theory. The force-matching procedure includes a fit of short-ranged nonbonded forces, bonded forces, and atomic partial charges. The various parameterizations of the water force field differ by an enforced smooth cut-off applied to the short-ranged interaction term. These were obtained by fitting to the trajectory and force data produced by Car-Parrinello MD simulations of systems of 32 and 64 H(2)O molecules. The new water force fields were developed assuming both flexible or rigid molecular geometry. The simulated structural and self-diffusion properties of liquid water using the fitted force fields are in close agreement with those observed in the underlying Car-Parrinello MD simulations. The resulting empirical models compare to experiment much better than many conventional simple point charge (SPC) models. The fitted potential is also shown to combine well with more sophisticated intramolecular potentials. Importantly, the computational cost of the new models is comparable to that for SPC-like potentials.

The quantum dynamics of an excess proton in water

The quantum dynamics and energetics of an excess proton in water have been studied computationally. Comparison of a quantum mechanical treatment of the transferring proton and the water solvent is made with a classical treatment of the same system. The exchange of the proton between two water molecules is found to be an activationless quantum process. Analysis of the microscopic structure of the solvent around the proton transfer complex is also carried out, and the quantum infrared spectrum of the transferring proton is calculated and analyzed in terms of Zundel polarization. The Grotthus mechanism for proton migration in water is also examined within the context of the model. Grotthus behavior is suggested to depend critically on the dynamics of water molecules in the second solvation shell of the H5O+2 complex, as well as the inward fluctuations of the oxygen–oxygen distance of water molecules that hydrogen bond to the H5O+2 complex in the first solvation shell. The quantum effects on the nuclear dynam...

Ab initio molecular dynamics: Propagating the density matrix with Gaussian orbitals. III. Comparison with Born-Oppenheimer dynamics

In a recently developed approach to ab initio molecular dynamics (ADMP), we used an extended Lagrangian to propagate the density matrix in a basis of atom centered Gaussian functions. Results of trajectory calculations obtained by this method are compared with the Born–Oppenheimer approach (BO), in which the density is converged at each step rather than propagated. For NaCl, the vibrational frequency with ADMP is found to be independent of the fictitious electronic mass and to be equal to the BO trajectory result. For the photodissociation of formaldehyde, H2CO→H2+CO, and the three body dissociation of glyoxal, C2H2O2→H2+2CO, very good agreement is found between the Born–Oppenheimer trajectories and the extended Lagrangian approach in terms of the rotational and vibrational energy distributions of the products. A 1.2 ps simulation of the dynamics of chloride ion in a cluster of 25 water molecules was used as a third test case. The Fourier transform of the velocity–velocity autocorrelation function showed ...