Force probe molecular dynamics simulations

J. Wang, R. J. Boyd, and A. Laaksonen, J. Cbem. Pbys., 104, 7261. A Hybrid Quantum Mechanical Force Field Molecular Dynamics Simulation of Liquid Methanol Vibrational Frequency Shifts as a Probe of the Quantum Mechanical/Molecular Mechanical Coupling. 

J. Wang, R.J. Boyd, and A. Laaksonen, A hybrid quantum mechanical force field molecular dynamics simulation of liquid methanol Vibrational fiie-quency shifts as a probe of the quantum mechanical molecular mechanical coupling, J. Chem. Phys., 104(1996), 7261-7269. 

Specific polarization effects, beyond those modelled by a continuum dielectric model and the movement of certain atoms, are neglected in MIF calculations. Many-body effects are also neglected by use of a pair-wise additive energy function. Polarizable force fields are, however, becoming more common in the molecular mechanics force fields used for molecular dynamics simulations, and MIFs could be developed to account for polarizability via changes in charge magnitude or the induction of dipoles upon movement of the probe. 

On the basis of our results using scanning force microscopy such as S VM and LFM, we claim that the mobility at the surface of PS films is not the same as that in the bulk. However, in such measurements, a probe tip made of silicon or silicon nitride makes contact with the surface to be measured. This may induce some artifacts in the results. If an effect of tip contact on the surface dynamics cannot be negligible, our conclusion must be reconsidered. Thus, T is here discussed on the basis of coarse-grained molecular dynamics simulation using a bead-spring model of Grest... 

In the oxygen VER experiments (3) the n = 1 vibrational state of a given oxygen molecule is prepared with a laser, and the population of that state, probed at some later time, decays exponentially. Since in this case tiojo kT, we are in the limit where the state space can be truncated to two levels, and 1/Ti k, 0. Thus the rate constant ki o is measured directly in these experiments. Our starting point for the theoretical discussion is then Equation (14). For reasons discussed in some detail elsewhere (6), for this problem we use the Egelstaff scheme in Equation (19) to relate the Fourier transform of the quantum force-force time-correlation function to the classical time-correlation function, which we then calculate from a classical molecular dynamics computer simulation. The details of the simulation are reported elsewhere (4) here we simply list the site-site potential parameters used therein e/k = 38.003 K, and a = 3.210 A, and the distance between sites is re = 0.7063 A. 

The first worker to consider the detailed effect of a strong external force field on the molecular dynamics of an isotropic molecular liquid seems to have been Benoit. This treatment may be developed considerably and extended. In this review, however, the technique of computer simulation is used in combination with reduced model theory (see Chapter I) in an attempt to probe more deeply into the fundamental physical characteristics of the molecular liquid state. 

B. A. Heymann and H. Grubmiiller (2001) Molecular dynamics force probe simulations of antibody/antigen unbinding Entropic control and nonadditivity of unbinding forces. Biophys. J. 81, pp. 1295-1313... 

The atomistic structure and dynamics of the interaction of an atomic force microscopic probe (AFM) with a crystalline polyethylene surface was examined by using the molecular dynamics method coupled with ab initio quantum calculations [21]. A set of force parameters and guidelines have been derived from the extensive computer simulations, and these results were used to help explain some of the AFM images. In general, AFM experiments can be performed in a nondestructive mode with a reasonable resolution, provided that the forces of interaction between a typical-size tip and sample are kept within the... 

As was the case for XANES, here electronic structure calculations including solvent effects are used to draw conclusions on the most probable coordination isomer and from that structure the interatomic bond distances can be directly compared to the computed EXAFS spectra [150-152]. As EXAFS spectroscopy probes the structure of a statistically averaged system, the most appropriate way of comparing theoretical EXAFS data to experimental ones is to use molecular dynamics trajectories to sample the configuration space, select snapshots and finally compute a statistically average spectrum [89,153] with a direct estimate of the mean square relative disorder (MSRD, also called or the EXAFS Debye-Waller term). However, as discussed in Section 11.2.3, the relevance of MD simulations hinges on how accurate intermolecular interactions are, given that these are usually obtained at DFT level (in Car-Parinello MD simulations) or with force-fields (in classical MD simulations). 

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