Force field customization

It is occasionally desirable to add new parameters to a molecular mechanics force field. This might mean adding an element that is not in the parameterization set or correctly describing a particular atom in a specihc class of molecules. 

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In our implementation of SMD, modified versions of VMD and Sigma communicate with each other using a customized, lightweight protocol. Sigma sends atomic positions resulting from each molecular dynamics time step to VMD for display. When the user specifies restraints on parts of the displayed model, VMD sends them to Sigma, where they are converted into potential-well restraints added to the force field [21]. 

Most existing molecular mechanics studies of inorganic molecules required careful customization of force field parameters. 

Chem3D uses a MM2 force field that has been extended to cover the full periodic table with the exception of the /block elements. Unknown parameters will be estimated by the program and a message generated to inform the user of this. MM2 can be used for both energy minimization and molecular dynamics calculations. The user can add custom atom types or alter the parameters used... 

There are many different pieces of code available for molecular mechanics, ranging from the simple, such as MM2, to the elaborate, such as Cerius S YBYL, Spartan, and HyperChem. The code chosen for a particular model of catalytic processes depends on two factors (1) the complexity of the system that is to be studied, and (2) the amount of computer expertise available. Complicated structures, such as surfaces and zeolites, generally require specialized software packages for their visualization typically workers use commercial code with perhaps minor modifications. Simpler systems, such as modeling vanadium oxo species, are amenable to study using simpler codes, such as MM2, that are customized to suit the specific needs of the research group. It should be noted that the various available packages employ different force assumptions and some force fields are more suitable to one kind of application than to another (see Chapter 2). 

The need for high-quality force field parameters is critical to rapidly generate accurate smaU-molecule conformations, which are needed for reliable computational CSP. In this chapter, we presented specific force field improvements that lead to better smaU-molecule conformations for close S O and halogen X - O interactions. We customized the force field by fitting to quantum mechanical data and comparing with conformations from the CSD, which is a general approach that can be extended... 

Nonbonded terms typically include steric (e.g., van der Waals) and electrostatic (e.g., Coulombic) terms but may also include polarization contributions. Force field parameters for each bonded or nonbrmded term are obtained by fitting potential energy terms to ab initio (e.g., HF/6-31G ) or DFT calculations of small molecules or by fitting to experimental data such as crystal structure and the heat of vaporization (A/fy) for low-molecular-weight compounds. The form of specific terms used by different commercial, public domain, and customized force fields for polymer simulations are given in the sections that follow. 

The most basic approach to carry out MD simulations for larger systems is to use classical force fields. A variety of different force fields for molecular mechanics (MM) simulations has been developed,which are mainly intended to describe the non-reactive dynamics of large systems. In particular in the field of biochemistry force fields play an essential role to study the complex properties of large biomolecules. However, classical force fields require the specification of the connectivity of the atoms. Therefore, they are not able to describe chemical reactions, i.e., the making and breaking of bonds. To describe reactions, they can be combined with quantum mechanical (QM) methods in so-called QM/MM simulations. In recent years also reactive force fields , e.g. ReaxFF, have been introduced, which overcome this limitation. However, these reactive force fields are typically highly adapted to specific systems by analytic terms customized to describe e.g. certain bonding situations, and only a few applications have been reported so far. 

It is axiomatic that sales analysis depends on detailed records of sales of a specific chemical to a specific company. Paramount to the success of such studies is the existence of data recorded on a systematic and continuous basis. It follows that these studies are done best by an ia-house staff on products already produced by the company. However, on occasion, a product new to the company can be studied by the ia-house group with the assistance of their field sales force. For example, a producer of polypropylene could use its people to secure data on the consumption of other thermoplastics by their customers. Such an exercise might identify opportunities for a new producer, but a more detailed marketing research study would probably be done before entry iato the new product area was made. 

Advances in polymer and fibre science and in the manufacturing technologies of fibres, yarns and fabrics have been the driving force behind the development of smart textiles and innovative products that fulfil customer expectations. In contrast with the situation that existed 20years ago, these products now find applications primarily in sectors outside the textile field. Therefore, fibre, yam and clothing producers are in constant pursuit of developing new materials in order to meet the demands for both traditional and technical textiles to be used for applications outside the textile industry. 

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