Adjustable Density Matrix Assembler ADMA method

The Mulliken-Mezey AFDF scheme and the more general AFDF schemes - also serve as the basis for the adjustable density matrix assembler (ADMA) method. The ADMA method generates ab initio quality macromolecular density matrices, which can be used for the computation of a variety of ab initio quality properties for macromolecules. The ADMA method is also suitable for the calculation of ab initio quality electronic densities, however, additional molecular properties, such as forces and energies, can also be calculated. These options of the ADMA method are expected to be useful in macromolecular conformational analysis, geometry optimizations, and in computational studies of protein folding. 

Fragmentation (AFDF) Principle, and the Adjustable Density Matrix Assembler (ADMA) Method. 172... 

Specific aspects of the quantum chemical concept of local electron densities and functional groups of chemistry have been discussed, with emphasis on the Additive Fuzzy Density Fragmentation (AFDF) Principle, on the Adjustable Density Matrix Assembler (ADMA) Method of using a local density matrix formalism of fuzzy electron density fragments in macromolecular quantum chemistry, and on the fundamental roles of the holographic electron density theorem, local symmetry, and symmetry deficiency. 

Electron density decreases exponentially with distance that suggests that an Additive Fuzzy Density Fragmentation (AFDF) approach can be used for both a fuzzy decomposition and construction of molecular electron densities. The simplest AFDF technique is the Mulliken-Mezey density matrix fragmentation [12,13], that is the basis of both the Molecular Electron Density Loge Assembler (MEDLA) [14-17] and the Adjustable Density Matrix Assembler (ADMA) [18-21] macromolecular quantum chemistry methods. 

A more advanced AFDF approach, the ADMA method (Adjustable Density Matrix Assembler method) [39-41] is based on a density matrix database and the actual construction of a macromolecular density matrix. This technique, also reviewed in part in ref.[31], is suitable for the rapid computation of various additional molecular properties besides electron densities. 

Some recent developments concerning macromolecular quantum chemistry, especially the first linear-scaling method applied successfully for the ab initio quality quantum-chemistry computation of the electron density of proteins, have underlined the importance and the applicability of quantum chemistry-based approaches to molecular similarity. These methods, the linear-scaling numerical Molecular Electron Density Lego Approach (MEDLA) method [6 9] and the more advanced and more generally applicable linear-scaling macromolecular density matrix method called Adjustable Density Matrix Assembler or ADMA method [10,11], have been employed for the calculation of ab initio quality protein electron densities and other... 

The same Mulliken-Mezey method, and the more elaborate alternative partitioning schemes serve as the basis of the ALDA (adjustable local density assembler) method and the ADMA (adjustable density matrix assembler) technique. The ALDA and ADMA methods generate geometry-adjustable electronic densities and macromolecular density matrices. The ADMA macromolecular density matrices can be computed without determining a macromolecular wave function, a feature advantageous in the macromolecular application of a variety of quantum-chemical... 

ADMA = adjustable density matrix assembler AFDF = additive fiizzy density fragmentation GSTE = geometrical similarity as topological equivalence MEDLA = molecular electron density loge assembler MEP = molecular electrostatic potential RBSM = resolution-based similarity measures SGM = shape group methods VDWS = van der Waals surface ID, 2D, 3D = one, two, and three dimensions. 

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