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• W2085471424 abstract "The major decisions affecting the construction of a general purpose molecular mechanics program are discussed, although care is taken to highlight techniques which may be useful in special cases. The choice of co-ordinate system, cartesian or internal, in which minimization is to be affected is largely a matter of personal preference as there is little to choose between the two options as far as speed or performance are concerned, although cartesians are probably slightly easier to program. Minimization algorithms based on the general Newton iteration, are the logical, and for practical purposes the only, choice of procedure. In order to obtain consistent and reliable results the maximum net force on any one atom at the local energy minimum should be less than 10−6 kcal mole−1 Å−1 and this can only be achieved by means of a second derivative or quasi-Newton minimization algorithm. The latter techniques are rather sensitive to poor approximations to the minimum energy molecular conformation and may be profitably used in tandem with algorithms (pattern search, steepest descent, etc.) which have poorer convergence properties but are more tolerant of approximate trial structures. The choice of analytical or numerical derivatives to be used in conjunction with the (Newton iteration-based) minimization procedure is again something of an open question-analyticals are faster but numericals easier to program and more versatile. With care, numerical first and second derivatives can be calculated only marginally more slowly than analyticals and ways of achieving this are discussed. Calculation of transition states and a procedure midway between trial and error and least-squares generation of force fields are also discussed. Finally the program which resulted from the foregoing considerations is described and an indication of storage requirements and program performance is given. The program uses cartesian co-ordinates, a tandem quasi-Newton minimization procedure and numerical first and second derivatives." @default.
• W2085471424 created "2016-06-24" @default.
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• W2085471424 date "1977-01-01" @default.
• W2085471424 modified "2023-10-14" @default.
• W2085471424 title "The principles and practice of molecular mechanics calculations" @default.
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• W2085471424 doi "https://doi.org/10.1016/0097-8485(77)85014-6" @default.
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