Direct determination of discrete harmonic bath parameters from molecular dynamics simulations

We present a direct procedure for determining the parameters of a discrete harmonic bath modeling the influence of a complex condensed phase environment on the system of interest. The procedure employs an efficient discretization of the spectral density into modes that correspond to equal fractions of the reorganization energy. The new procedure uses directly the classical correlation function (available from molecular dynamics calculations) as input, avoiding numerical computation of the spectral density by means of a discrete Fourier transform. Convergence is obtained using a shorter time length of the correlation function, leading to significant computational savings. © 2016 Wiley Periodicals, Inc.     

Dimer models for ErbB-2/neu transmembrane domains from molecular dynamics simulations

Interest in the transmembrane receptors tyrosine kinase of the erbB family is high due to the involvement of some of the members in human cancers. The original oncogenic alleles of neu discovered in rat neuroectodermal tumors lead to single Val664Glu substitution within the predicted transmembrane domain. Identical substitution at the homologous position 659 constitutively activates the oncogenic potential of the human ErbB-2 receptor by enhanced receptor dimer formation. The precise molecular details of receptor dimerization are still unknown and to acquire more knowledge of the mechanisms involved, molecular dynamics simulations are undertaken to study transmembrane dimer association. Transmembrane helices are predicted to associate in left-handed coiled-coil structures stabilized by Glu-Glu interhelix hydrogen bonds in the mutated form. The internal dynamics reveals π helix deformations which modify the helix-helix interface. Predicted models agree with those suggested from polarized IR and magic-angle spinning NMR spectroscopy. Received: 24 April 1998 / Accepted: 17 September 1998 / Published online: 10 December 1998     

Vesicle shapes from molecular dynamics simulations

Lipid bilayer membranes are known to form various structures such as large sheets or vesicles. When the two leaflets of the bilayer have an equal composition, the membrane preferentially forms a flat sheet or a spherical vesicle. However, a difference in the composition of the two leaflets may result in a curved bilayer or in a wide variety of vesicle shapes. Vesicles with different shapes have already been shown in experiments and diverse vesicle shapes have been predicted theoretically from energy minimization of continuous curves. Here we present a molecular dynamics study of the effect of small changes in the phospholipid headgroups on the spontaneous curvature of the bilayer and on the resulting vesicle shape transformations. Small asymmetries in the bilayers already result in high spontaneous curvature and large vesicle deformations. Vesicle shapes that are formed include ellipsoids, discoids, pear-shaped vesicles, cup-shaped vesicles, as well as budded vesicles. Comparison of these vesicles with theoretically derived vesicle shapes shows both resemblances and differences.     

Estimating entropies from molecular dynamics simulations

While the determination of free-energy differences by MD simulation has become a standard procedure for which many techniques have been developed, total entropies and entropy differences are still hardly ever computed. An overview of techniques to determine entropy differences is given, and the accuracy and convergence behavior of five methods based on thermodynamic integration and perturbation techniques was evaluated using liquid water as a test system. Reasonably accurate entropy differences are obtained through thermodynamic integration in which many copies of a solute are desolvated. When only one solute molecule is involved, only two methods seem to yield useful results, the calculation of solute-solvent entropy through thermodynamic integration, and the calculation of solvation entropy through the temperature derivative of the corresponding free-energy difference. One-step perturbation methods seem unsuitable to obtain entropy estimates.     

Paramfit: Automated optimization of force field parameters for molecular dynamics simulations

The generation of bond, angle, and torsion parameters for classical molecular dynamics force fields typically requires fitting parameters such that classical properties such as energies and gradients match precalculated quantum data for structures that scan the value of interest. We present a program, Paramfit, distributed as part of the AmberTools software package that automates and extends this fitting process, allowing for simplified parameter generation for applications ranging from single molecules to entire force fields. Paramfit implements a novel combination of a genetic and simplex algorithm to find the optimal set of parameters that replicate either quantum energy or force data. The program allows for the derivation of multiple parameters simultaneously using significantly fewer quantum calculations than previous methods, and can also fit parameters across multiple molecules with applications to force field development. Paramfit has been applied successfully to systems with a sparse number of structures, and has already proven crucial in the development of the Assisted Model Building with Energy Refinement Lipid14 force field. © 2014 Wiley Periodicals, Inc.     

Insights into intrastrand cross-link lesions of DNA from QM/MM molecular dynamics simulations

DNA damages induced by oxidative intrastrand cross-links have been the subject of intense research during the past decade. Yet, the currently available experimental protocols used to isolate such lesions only allow to get structural information about linked dinucleotides. The detailed structure of the damaged DNA macromolecule has remained elusive. In this study we generated in silico the most frequent oxidative intrastrand cross-link adduct, G[8,5-Me]T, embedded in a solvated DNA dodecamer by means of quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations. The free energy of activation required to bring the reactant close together and to form the C-C covalent-bond is estimated to be ~10 kcal/mol. We observe that the G[8,5-Me]T tandem lesion is accommodated with almost no perturbation of the Watson-Crick hydrogen-bond network and induces bend and unwinding angles of ~20° and 8°, respectively. This rather small structural distortion of the DNA macromolecule compared to other well characterized intrastrand cross-links, such as cyclobutane pyrimidines dimers or cisplatin-DNA complex adduct, is a probable rationale for the known lack of efficient repair of oxidative damages.     

Charge distributions for molecular dynamics simulations from self-consistent polarization method

Partial atomic charges are important force field parameters. They are usually computed by applying quantum-chemical calculations and the assumed population scheme. In this study polarization consistent scheme of deriving a charge distribution inside solute molecule is proposed. The environment effect is explicitly taken into account by distributing solvent molecules around the solute target. The performed analysis includes a few computational schemes (HF, MP2, B3LYP, and M026X), basis sets (cc-pvnz, n = 2, 3, …, 6), and electrostatically derived charge distributions (KS, CHELP, CHELPG, and HLY). It is demonstrated that the environment effect is very important and cannot be disregarded. The second solvation shell should be included to achieve the charge convergence. Huge corrections to charge distribution are due to induction and dispersion. The B3LYP/cc-pvqz level of theory is recommended for deriving the charges within self-consistent polarization scheme.     

Determining equilibrium constants for dimerization reactions from molecular dynamics simulations

With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices covers sufficiently many dimerization and dissociation events, their binding free energy is readily derived from the fraction of time during which the two helices are observed in dimeric form. Exactly how the correct value for the free energy is to be calculated, however, is unclear, and indeed several different and contradictory approaches have been used. In particular, results obtained via Boltzmann statistics differ from those determined via the law of mass action. Here, we develop a theory that resolves this discrepancy. We show that for simulation systems containing two molecules, the dimerization free energy is given by a formula of the form ΔG ∝ ln(P(1) /P(0) ). Our theory is also applicable to high concentrations that typically have to be used in molecular dynamics simulations to keep the simulation system small, where the textbook dilute approximations fail. It also covers simulations with an arbitrary number of monomers and dimers and provides rigorous error estimates. Comparison with test simulations of a simple Lennard Jones system with various particle numbers as well as with reference free energy values obtained from radial distribution functions show full agreement for both binding free energies and dimerization statistics.     

Insights into uranyl chemistry from molecular dynamics simulations

First-principles and purely classical molecular dynamics (MD) simulations for complexes of the uranyl ion (UO(2)(2+)) are reviewed. Validation of Car-Parrinello MD simulations for small uranyl complexes in aqueous solution is discussed. Special attention is called to the mechanism of ligand-exchange reactions at the uranyl centre and to effects of solvation and hydration on coordination and structural properties. Large-scale classical MD simulations are surveyed in the context of liquid-liquid extraction, with uranyl complexes ranging from simple hydrates to calixarenes, and nonaqueous phases from simple organic solvents and supercritical CO(2) to ionic liquids.     

Micellar crystals in solution from molecular dynamics simulations

Polymers with both soluble and insoluble blocks typically self-assemble into micelles, which are aggregates of a finite number of polymers where the soluble blocks shield the insoluble ones from contact with the solvent. Upon increasing concentration, these micelles often form gels that exhibit crystalline order in many systems. In this paper, we present a study of both the dynamics and the equilibrium properties of micellar crystals of triblock polymers using molecular dynamics simulations. Our results show that equilibration of single micelle degrees of freedom and crystal formation occur by polymer transfer between micelles, a process that is described by transition state theory. Near the disordered (or melting) transition, bcc lattices are favored for all triblocks studied. Lattices with fcc ordering are also found but only at lower kinetic temperatures and for triblocks with short hydrophilic blocks. Our results lead to a number of theoretical considerations and suggest a range of implications to experimental systems with a particular emphasis on Pluronic polymers.     

Dissociative water potential for molecular dynamics simulations

A new interatomic potential for dissociative water was developed for use in molecular dynamics simulations. The simulations use a multibody potential, with both pair and three-body terms, and the Wolf summation method for the long-range Coulomb interactions. A major feature in the potential is the change in the short-range O-H repulsive interaction as a function of temperature and/or pressure in order to reproduce the density-temperature curve between 273 K and 373 at 1 atm, as well as high-pressure data at various temperatures. Using only the change in this one parameter, the simulations also reproduce room-temperature properties of water, such as the structure, cohesive energy, diffusion constant, and vibrational spectrum, as well as the liquid-vapor coexistence curve. Although the water molecules could dissociate, no dissociation is observed at room temperature. However, behavior of the hydronium ion was studied by introduction of an extra H+ into a cluster of water molecules. Both Eigen and Zundel configurations, as well as more complex configurations, are observed in the migration of the hydronium.     

Nucleation rate isotherms of argon from molecular dynamics simulations

We report six nucleation rate isotherms of vapor-liquid nucleation of Lennard-Jones argon from molecular dynamics simulations. The isotherms span three orders of magnitude in nucleation rates, 10(23)相似文献