Running, trajectory

A, and the potential surface Eg. Estimate the time f, as discussed in the caption of Fig. 3.7. You may also accomplish this by using the potential e = (e2 + j)/2, running trajectories on this potential until equilibration, and then changing e to Eg. If you have difficulties generating the potential Eg or its first derivatives, use for simplicity the potential ex (which will give, however, somewhat too small value for f). 

Figure 15. Frequency distribution of the number of negative eigenvalues in the Hessian matrix of the potential function that are counted along running trajectories. The solid, dotted, and dot-dashed lines are, respectively for the energies —ll.Oe, -11.5e, and -12.0e. (Reproduced from Ref. 11 with permission.)...

The analytical derivatives of the potential surface allow a sampling of the EVB energy surface by MD simulations. In principle, running MD trajectories on the EVB surface of the reactant state can provide the free energy function that is needed to calculate the activation free energy. In order to reach the TS, it becomes necessary to run trajectories on a series of potential surfaces ( mapping potentials) that drive the system adiabatically from the reactant to the product state. In the simple case of two diabatic states the mapping potential (em) can be written as a linear combination of the reactant and product potentials, and s2 ... 

A clear picture of the difference in dynamics between bulk water and biological water can be seen in Figure 6.1. Here we plot the running trajectory of the angular displacement of a randomly chosen and tagged water molecule, separately for one in bulk water and one on the surface of a protein. The tagged water molecule is at the surface of a protein lysozyme. In bulk, a water molecule undergoes frequent... 

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