Force field comparison

Zgarbova M et al (2010) Large-scale compensation of errors in pairwise-additive empirical force fields comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations. Phys Chem Chem Phys 12 10476-10493... 

Geometry optimization of cyclohexane (force fields comparison)... 

Force fields are empirically based functions that use experimentally derived parameters for the bond lengths, angles, and force constants. Parameters are typically obtained from small organic molecules or, where experimental data are undetermined, can be calculated using ab initio methods.Ffence, force fields have their limitations, and there have been many force field comparisons performed to assess their accuracy and abilities.Arguably, a stronger assessment of a force field is whether it is able to adequately reproduce experimental observables. It is important to note that many of the force... 

Large stepsizes result in a strong reduction of the number of force field evaluations per unit time (see left hand side of Fig. 4). This represents the major advantage of the adaptive schemes in comparison to structure conserving methods. On the right hand side of Fig. 4 we see the number of FFTs (i.e., matrix-vector multiplication) per unit time. As expected, we observe that the Chebyshev iteration requires about double as much FFTs than the Krylov techniques. This is due to the fact that only about half of the eigenstates of the Hamiltonian are essentially occupied during the process. This effect occurs even more drastically in cases with less states occupied. 

The fifth and final chapter, on Parallel Force Field Evaluation, takes account of the fact that the bulk of CPU time spent in MD simulations is required for evaluation of the force field. In the first paper, BOARD and his coworkers present a comparison of the performance of various parallel implementations of Ewald and multipole summations together with recommendations for their application. The second paper, by Phillips et AL., addresses the special problems associated with the design of parallel MD programs. Conflicting issues that shape the design of such codes are identified and the use of features such as multiple threads and message-driven execution is described. The final paper, by Okunbor Murty, compares three force decomposition techniques (the checkerboard partitioning method. 

A force field does not consist only of a mathematical eiqjression that describes the energy of a molecule with respect to the atomic coordinates. The second integral part is the parameter set itself. Two different force fields may share the same functional form, but use a completely different parameterization. On the other hand, different functional forms may lead to almost the same results, depending on the parameters. This comparison shows that force fields are empirical there is no "correct form. Because some functional forms give better results than others, most of the implementations within the various available software packages (academic and commercial) are very similar. 

Variations of these releases are implemented in almost every commercial or academic software package, which cannot be fisted in this context. A comprehensive comparison of several force fields focusing the calculation of conformational energies of organic molecules has been published by Pettersson and liljefors [1]. 

I. Pettersson, T. Liljefors, Molecular mechanics calculated conformational energies of organic molecules a comparison of force fields, in Reviews in Computational Chemistry, Vbl. 9,... 

Previous investigations might influence the choice of a molecular mcch an ics m ethod. If tnolecu lar tncchan ics calcu lation s of a par-ticti lar com poun d or m olecule type already exist, choose the same force field so you can make comparisons easily. 

To date, a number of simulation studies have been performed on nucleic acids and proteins using both AMBER and CHARMM. A direct comparison of crystal simulations of bovine pancreatic trypsin inliibitor show that the two force fields behave similarly, although differences in solvent-protein interactions are evident [24]. Side-by-side tests have also been performed on a DNA duplex, showing both force fields to be in reasonable agreement with experiment although significant, and different, problems were evident in both cases [25]. It should be noted that as of the writing of this chapter revised versions of both the AMBER and CHARMM nucleic acid force fields had become available. Several simulations of membranes have been performed with the CHARMM force field for both saturated [26] and unsaturated [27] lipids. The availability of both protein and nucleic acid parameters in AMBER and CHARMM allows for protein-nucleic acid complexes to be studied with both force fields (see Chapter 20), whereas protein-lipid (see Chapter 21) and DNA-lipid simulations can also be performed with CHARMM. 

It is important to mention that for most applications the special form of the force field is not as important as the actual values of the parameters. These parameters are determined in a number of ways, mainly by comparison with experiments, e.g., vibrational spectroscopy. Torsional potentials, which are crucial for polymer configurations and dynamics of polymers, can... 

FIG. 2 Growth rates as a function of the driving force A//. Comparison of theory and computer simulation for different values of the diffusion length and at temperatures above and below the roughening temperature. The spinodal value corresponds to the metastability limit A//, of the mean-field theory [49]. The Wilson-Frenkel rate WF is the upper limit of the growth rate. 

Table 2.3 Comparison of functional forms used in common force fields. The torsional energy, [ors is in all cases given as a Fourier series in the torsional angle...

Finally, force field methods are zero-dimensional . It is not possible to asses the probable error of a given result within the method. The quality of the result can only be judged by comparison with other calculations on similar types of molecules, for which relevant experimental data exist. 

IR absorptions of these species were assigned to fundamental modes by comparison with the spectra of stable perfluoroorganic compounds. Normal coordinate analysis of the perfluoroethyl radical was performed and the valence force field of C2F5 was calculated (Snelson et al., 1981). 

Based both on the determined isotopic shifts and the comparison of the radical IR spectrum with the spectra of various substituted benzenes, the bands have been assigned to the normal modes and the force field of the benzyl radical calculated (Table 8). 

The first-principles calculation of NIS spectra has several important aspects. First of all, they greatly assist the assignment of NIS spectra. Secondly, the elucidation of the vibrational frequencies and normal mode compositions by means of quantum chemical calculations allows for the interpretation of the observed NIS patterns in terms of geometric and electronic structure and consequently provide a means of critically testing proposals for species of unknown structure. The first-principles calculation also provides an unambiguous way to perform consistent quantitative parameterization of experimental NIS data. Finally, there is another methodological aspect concerning the accuracy of the quantum chemically calculated force fields. Such calculations typically use only the experimental frequencies as reference values. However, apart from the frequencies, NIS probes the shapes of the normal modes for which the iron composition factors are a direct quantitative measure. Thus, by comparison with experimental data, one can assess the quality of the calculated normal mode compositions. 

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