QM/MD simulation

At several points in diis book, it has been emphasized that the prevalence of classical MC and MD simulations derives from die impracticality of carrying out fully QM dynamics. While diis is largely true, for systems of only modest size where short trajectories may be profitably analyzed, fully QM MD simulations using the so-called Car-Parrinello technique are a viable option (Car and Parrinello 1985). In its most widely used formulation, the Car-Parrinello method employs DFT as the electronic-structure method of choice. In... 

QM/MD Simulations of High-Temperature SWCNT Self-capping... 

We have performed simulations of the thermally activated self-capping process of carbon-only (CUT) and edge-oxidized (OX) models of open-ended SWCNTs, using quantum chemical molecular dynamics (QM/MD) simulations. We observed the following important features in trajectories up to 150 picoseconds ... 

Irle S, Zheng G, Wang Z, Morokuma K (2006) The Ceo formation puzzle solved QM/MD simulations reveal the shrinking hot giant road of the dynamic fuUerene self-assembly mechanism. J Phys Chem B 110 14531-14545... 

Fig. 31.2. DFTB QM/MD simulation of a (5,5) open-ended SWNT of 7.5 A length at 3000 K. Wobbling Cj units are the predominant structural feature of this type of system, not at all appearing in comparable REBO type simulations (see Fig. 31.3).

Solution Ab Initio QM/MM MD Simulations. Journal of the American Chemical Society, 126, 2582-2587. 

Relative free energy changes along the reaction coordinate may be calculated via MD simulations. Subsequently, they may be combined with the QM total energies of the reacting QM subsystem to obtain the overall free energy profiles associated with the reaction steps in the following way... 

The free energy differences A qm/mm m) between different images along the path are calculated using MD simulations and the FEP theory [38],... 

In order to better understand these results we have compared the results from the first step of these paths (paths A and D respectively) to a previously obtained path (path B) which was calculated with the combined procedure [35], In the case of path B, the enzyme environment has been relaxed by MD simulations and QM/MM optimizations as explained in Section 3.2.5. Additionally, we have also calculated a... 

As discussed in many previous studies of biomolecules, the treatment of electrostatic interactions is an important issue [69, 70, 84], What is less widely appreciated in the QM/MM community, however, is that a balanced treatment of QM-MM electrostatics and MM-MM electrostatics is also an important issue. In many implementations, QM-MM electrostatic interactions are treated without any cut-off, in part because the computational cost is often negligible compared to the QM calculation itself. For MM-MM interactions, however, a cut-off scheme is often used, especially for finite-sphere type of boundary conditions. This imbalanced electrostatic treatment may cause over-polarization of the MM region, as was first discussed in the context of classical simulations with different cut-off values applied to solute-solvent and solvent-solvent interactions [85], For QM/MM simulations with only energy minimizations, the effect of over-polarization may not be large, which is perhaps why the issue has not been emphasized in the past. As MD simulations with QM/MM potential becomes more prevalent, this issue should be emphasized. 

In order to ensure accurate CG potentials, one needs to conduct MD simulations with a reliable atomistic potential model. The most desirable theoretical approach for the atomistic-scale simulations would be to use a level of quantum mechanics (QM) that can treat both intermolecular and intramolecular interactions with acceptable accuracy. Realistically, the minimal QM levels of theory that can adequately treat all different types of chemical forces are second order perturbation theory [32] (MP2)... 

The above discussion sets the stage for the type of QM-MM studies we have performed for tryptophan in proteins. The use of MD simulations to study membranes is now a mature field, and has recently been reviewed in the context of the present book by Demchenko and Yesylevskyy [82]. A number of questions might be answered regarding details of the mechanism of voltage-sensitive dyes by... 

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