Force fields programs, development

The program and force field SHAPES, developed for transition metal complexes and tested for square planar geometries, uses a single Fourier term (Eq. 2.19), which is similar to the torsional angle term in many molecular mechanics programs (see Section 2.2.3 periodicity = m, phase shift = Fourier force constant kg is related to that of the harmonic potential, kg (Eq. 2.7) by Eq. 2.20. 

The program and force field SHAPES, developed for transition metal complexes and tested for square-planar geometries, uses a single Fourier term (Eq. 

It is beyond the scope of this short review to list every available molecular mechanics program. Only a selected few programs are mentioned here, without descriptive details of the potential functions, minimization algorithms, or comparative evaluations. Both the CHARMM and AMBER force fields use harmonic potential functions to calculate protein structures. They were developed in the laboratories of Karplus and Kollman, respectively, and work remarkably well. The CFF and force fields use more complex potential functions. Both force fields were developed in commercial settings and based extensively or exclusively on results obtained from quantum mechanics. Unlike the other molecular mechanics methods, the OPLS force field was parameterized by Jorgensen to simulate solution phase phenomena. 

Examples of united-atom protein force-fields for proteins are GROMOS87 and 96,21,48 CHARMM PARAM19,49 OPLS/UA (united atom)50 and the original force fields developed for the AMBER program.51 United atom force fields were developed to reduce the computer time required for molecular dynamics simulations by reducing the number of atoms. They are still... 

Another example is a paper with Gelin on acetylcholine in which they also describe the use of a version of the consistent force field program. They develop a parameter set for a MUBPP by fitting, not optimisation. An important detail is emphasized minimisation under relaxation in all degrees of freedom is imperative for mean-... 

A crucial point is the use of a reliable force field, and various parameters for Ni11 have been developed and employed successfully 379,386-392 As an example, molecular mechanics calculations (MOMEC87 program) have been used to predict the isomer distributions of Ni11 complexes of chiral (95) and (96), and isomer ratios were in good agreement with observed ratios.393... 

There are many different molecular mechanics force fields available. Many of them were originally developed in academic laboratories to solve specific problems. For example, some were designed to handle small molecules while others were developed to deal with protein structures. Today, the original demarcation between macromolcules and small molecules has become blurred, and they now are commercially available. Initially, many molecular mechanics programs were distributed at nominal costs, but due to the lack of federal funding for most molecular mechanics... 

The study of the enantioselective hydrosilylation reaction was performed with a series of combined quantum mechanics/molecular mechanics (QM/MM) calculations [26, 30] within the computational scheme of ab initio (AIMD) (Car-Parrinello) [62] molecular dynamics. The AIMD approach has been described in a number of excellent reviews [63-66], AIMD as well as hybrid QM/MM-AIMD calculations [26, 47] were performed with the ab initio molecular dynamics program CPMD [67] based on a pseudopotential framework, a plane wave basis set, and periodic boundary conditions. We have recently developed an interface to the CPMD package in which the coupling with a molecular mechanics force field has been implemented [26, 68],... 

The use of molecular mechanics calculations has become common practice in chemical research since the early 80s, when general-purpose force fields, incorporated into user-oriented computer programs, started to appear (Figure 1). As noted above, the most popular and extensively used force fields are undoubtedly those developed by Allinger s group, namely MMI (early 70s), MM2 (1977-) and, more recently, MM3 (1988-). 

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