Search results for "force field"
showing 10 items of 55 documents
Performance of Different Force Fields in Force Probe Simulations
2013
We present detailed force probe molecular dynamic simulations of mechanically interlocked dimeric calix[4]arene-catenanes, comparing the results obtained using three different commonly used force fields (GROMOS G53a5, OPLS-AA, and AMBER GAFF). The model system is well characterized as a two-state system consisting of a closed compact and an elongated structure. Both states are stabilized by a different hydrogen-bond network, and complete separation of the dimer is prevented by the mechanical lock of the entangled aliphatic loops. The system shows fully reversible rebinding meaning that after bond rupture the system rejoins when the external force is relaxed. We present a detailed study of q…
Comparison of model potentials for molecular-dynamics simulations of silica.
2005
Structural, thermomechanical, and dynamic properties of pure silica SiO2 are calculated with three different model potentials, namely, the potential suggested by van Beest, Kramer, and van Santen (BKS) [Phys. Rev. Lett. 64, 1955 (1990)], the fluctuating-charge potential with a Morse stretch term for the short-range interactions proposed by Demiralp, Cagin, and Goddard (DCG)[Phys. Rev. Lett. 82, 1708 (1999)], and a polarizable force field proposed by Tangney and Scandolo (TS) [J. Chem. Phys. 117, 8898 (2002)]. The DCG potential had to be modified due to flaws in the original treatment. While BKS reproduces many thermomechanical properties of different polymorphs rather accurately, it also sh…
Vibrational Dynamics of Histamine Monocation in Solution: An Experimental (FT-IR, FT-Raman) and Theoretical (SCRF-DFT) Study
2000
spectra of histamine monocation in solution, based on the isotopic shifts and a previous vibrational study in solid state. Force field and normal coordinate calculations were computed to support these assignments. The ab initio force constants were transformed into a set of locally symmetrized internal coordinates and subsequently scaled to the experimental frequencies by using one specific and two generic scaling factors. The comparison in terms of vibrational frequencies and normal coordinate descriptions supported most of the proposed assignments. The theoretical infrared spectra for the two isotopomers on the basis of the ab initio intensities also showed a good correlation with the exp…
Electromechanics of graphene spirals
2014
Among the most fascinating nanostructure morphologies are spirals, hybrids of somewhat obscure topology and dimensionality with technologically attractive properties. Here, we investigate mechanical and electromechanical properties of graphene spirals upon elongation by using density-functional tight-binding, continuum elasticity theory, and classical force field molecular dynamics. It turns out that electronic properties are governed by interlayer interactions as opposed to strain effects. The structural behavior is governed by van der Waals interaction: in its absence spirals unfold with equidistant layer spacings, ripple formation at spiral perimeter, and steadily increasing axial force;…
The Right Answer for the Right Electrostatics: Force Field Methods Are Able to Describe Relative Energies of DNA Guanine Quadruplexes
2014
Different force fields and approximate density functional theory were applied in order to study the rotamer space of the telomeric G-quadruplex DNA. While some force fields show an erratic behavior when it comes to the reproduction of the higher-order DNA conformer space, OPLS and MMFF implementations are able to reproduce the experimentally known energy order. The stabilizing effect of the AA (anti−anti) versus SA (syn−anti) conformer is analyzed applying mechanical bond strength descriptors (compliance constants). The fact that we observe the correct energy order using appropriate force fields is in contrast with results previously reported, which suggested the general inappropriateness o…
Non Markovian Behavior of the Boltzmann-Grad Limit of Linear Stochastic Particle Systems
2007
We will review some results which illustrate how the distribution of obstacles and the shape of the characteristic curves influence the convergence of the probability density of linear stochastic particle systems to the one particle probability density associated with a Markovian process in the Boltzmann-Grad asymptotics.
Breakdown of the Reduction of the Rovibrational Hamiltonian: The Case of S18O2F2
2009
Abstract The ground state rotational spectrum of the near-spherical top molecule S18O2F2 (sulfuryl fluoride) has been measured from 50 to 700 GHz. As for the parent isotopologue, S16O2F2 [K. Sarka, J. Demaison, L. Margules, I. Merke, N. Heineking, H. Burger, H. Ruland, J. Mol. Spectrosc. 200 (2000) 55–64], it was necessary to use a non-reduced Hamiltonian in order to obtain a satisfactory fit. It was possible to determine six quartic centrifugal distortion constants (instead of five for a standard asymmetric top) and five sextic constants (one of them not existing in the reduced Hamiltonian) could also be determined. This ground state level has also been analysed thanks to a tensorial forma…
EnCurv: Simple Technique of Maintaining Global Membrane Curvature in Molecular Dynamics Simulations.
2021
The EnCurv method for maintaining membrane curvature in molecular dynamics simulations is introduced. The method allows maintaining any desired curvature in a sector of lipid membrane bent in a single plane without adding any unphysical interactions into the system and without restrictions on lateral and transversal lipid diffusion and distribution. The current implementation is limited to the membranes curved in a single plane but generalization to arbitrary curvature and membrane topology is possible. The method is simple, easy to implement, and scales linearly with the system size. EnCurv is agnostic to the force field, simulation parameters, and membrane composition. The proof of princi…
Simultaneous Determination of Force Constants and Dipole Moment Derivatives of Methane.
1998
The expressions of the effective Hamiltonian and dipole moment spectroscopic parameters in the tetrahedral formalism are used simultaneously to fit the force field and dipole moment derivatives of the methane molecule. Data, the so-called "observed parameters," are the values of the spectroscopic parameters determined from the frequencies and line strengths analyses. The ambiguities of most parameters (in the polyad scheme) are treated consistently with the Hamiltonian reduction chosen in the frequency analyses. As an illustration, the method is applied to the tetrahedral XY4 isotopic species only. The quadratic and cubic force field constants have been determined in addition to the linear …
New force field for GCMC simulations of D 2 /H 2 quantum sieving in pure silica zeolites
2020
International audience; We report a study on adsorption and coadsorption of H2 and D2 in FAU, MFI and CHA pure silica zeolites having different pore sizes and shapes. Adsorption capacities, selectivities, enthalpies and entropies are determined by combining experiments and GCMC simulations. We show that the force fields available in the literature cannot predict the adsorption equilibria below 77 K with sufficient accuracy. Here we propose a new force field adjusted by using our experimental data obtained for the pure silica MFI zeolite at 65 K and 77 K. With this new force field, it is possible to predict the adsorption and coadsorption equilibria on the three zeolite structures in a tempe…