Molecular dynamics force field development

M. A. Thompson, /. Phys. Chem., 99, 4794 (1995). Hybrid Quantum Mechanical-Molecular Mechanical Force Field Development for Large Flexible Molecules A Molecular Dynamics Study of 18-Crown-6. 

F. -Y. Dupradeau, and J. Kovensky, Multi-mannosides based on a carbohydrate scaffold Synthesis, force field development, molecular dynamics studies, and binding affinities for lectin Con A, J. Org. Chem., 72 (2007) 9032-9045. 

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 new parameter set for the MM2 force field, developed in an earlier work <2002PCA1266>, accurately predicted the conformational properties of 2-(2 -thienyl)-3-hexylthiophene 173, 2,5-bis(3 -hexyl-2 -thienyl)thio-phene 176, and 2,5-bis(4 -hexyl-2 -thienyl)thiophene 177. Thus, NOE buildup curves, calculated from average conformations obtained from molecular dynamics simulations, gave excellent or very good agreement with experimentally derived curves for almost all proton pairs. The averaging scheme for inter-proton distances... 

Specific polarization effects, beyond those modelled by a continuum dielectric model and the movement of certain atoms, are neglected in MIF calculations. Many-body effects are also neglected by use of a pair-wise additive energy function. Polarizable force fields are, however, becoming more common in the molecular mechanics force fields used for molecular dynamics simulations, and MIFs could be developed to account for polarizability via changes in charge magnitude or the induction of dipoles upon movement of the probe. 

Isothermal-isobaric molecular dynamics simulations of the a, p and 5 modifications have been carried out over the temperature range 4.2 - 553 K, using a force field developed for RDX, together with charges derived from ab initio calculations (Sorescu et al. 99ib). These gave results in close agreement with the experimentally determined crystal structures. Another molecular dynamics study (Kohno et al. 

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... 

Standard molecular mechanics (MM) methods (e.g. the popular force fields developed for AMBER, CHARMM and GROMOS decribed in Section 2 above) provide a good description of protein structure and dynamics, but cannot be used to model chemical reactions. This limitation is due their simple functional forms (e.g. harmonic terms for bond stretching) and inability to model changes in electronic polarization (because of the invariant point partial atomic charge used by these molecular mechanics methods to represent electrostatic interactions). 

One important point that we should bear in mind as we undertake a deeper analysis of molecular mechanics is that force fields are empirical-, there is no correct form for a force field. Of course, if one functional form is shown to perform better than another it is likely that form will be favoured. Most of the force fields in common use do have a very similar fqrm, and it is tempting to assume that this must therefore be the optimal functional form Certainly such models tend to conform to a useful picture of the interactions present in a system, but it should always be borne in mind that there may be better forms, particularly when developing a force field for new classes of molecule. The functional forms employed in molecular mechanics force fields are often a compromise between accuracy and computational efficiency the most accurate functional form may often be unsatisfactory for efficient computation. As the performance of computers increases so it becomes pcKsible to incorporate more sophisticated models. An additional consideration is that in order to use techniques such as energy minimisation and molecular dynamics, it is usually desirable to be able to calculate the first and second derivatives of the energy with respect to the atomic coordinates. 

Many different force fields are now available from commercial and other sources. Some force fields like the MM series of force fields developed by Allinger and the Merck MM [10] have been parameterized primarily for molecular mechanics and dynamics of small molecules. Due to their limited importance for polymer simulations, they will not be covered in this section however, they have been used to study conformational properties of model compounds for some aromatic polymers. In some cases, force fields primarily developed for biomolecules such as AMBER, CHARMM, and GROMOS have been used in the molecular simulation of polymeric systems. Force fields having particular importance for polymers include simple but versatile... 

Borodin O (2009) Polarizable force field development and molecular dynamics simulations of ionic liquids. J Phys Chem B 113 11463... 

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