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Furthermore, in certain cases it may be necessary to introduce another iterative cycle based on additional condensed phase simulations (loop IV, see below), although this is typically not required for the optimization of small-molecule parameters. 32 MacKerell With any iterative approach it is necessary to have convergence criteria in order to judge when to exit an iterative loop. In the case of the optimization of empirical force field parameters it is difficult to define rigorous criteria due to the often poorly defined and system-dependent nature of the target data; however, guidelines for such criteria are appropriate.

As mentioned above, the parameters should be optimized to reproduce the assignments of the frequencies as well as their numerical values. , symmetric methyl stretch, asymmetric stretch of water, and so on) are assigned to the individual frequencies [62,93]. The module MOLVIB [94] in CHARMM allows for calculation of PED for the empirically calculated vibrational spectra as well as for vibrational spectra calculated via QM calculations. Thus, the PED from the empirical vibrational spectra can be compared directly with assignments for experimental data based on isotopic substitution and/or QM-based assignments.

1 A than the QM values, especially in the analysis of data from MD simulations. For both energies and differences, the criteria presented above are with respect to the target data after they have been offset and scaled (see above). , Watson–Crick basepairs), the difficulty is again in selection of the appropriate target data, as with the conformational energetics discussed in the preceding paragraph, rather than the degree of convergence. Again, suitable experimental or QM data must be identified and then the empirical parameters must be optimized to reproduce both sets of data as closely as possible.

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