Programs in Physics & Physical Chemistry
|[Licence| Download | New Version Template] adid_v1_0.tar.gz(14 Kbytes)|
|Manuscript Title: ViPA: a computer program for vector projection analysis of normal vibrational modes of molecules.|
|Authors: A.K. Grafton, R.A. Wheeler|
|Program title: ViPA|
|Catalogue identifier: ADID_v1_0|
Distribution format: tar.gz
|Journal reference: Comput. Phys. Commun. 113(1998)78|
|Programming language: Fortran.|
|Computer: IBM RS6000.|
|Operating system: Unix: AIX 3.2.5, AIX 4.1, IRIX 5.2, IRIX 6.1.|
|Keywords: Normal modes, Vibration, Mode assignment, Isotopic substitution, Projection, Dot product, Molecular physics.|
Nature of problem:
Provide a quantitative comparison of the normal vibrational modes  of similar molecules, including molecules related by a perturbation of atomic masses, chemical bonding, electronic states, non-covalent contacts or some other factor. This virtually automates the process of transferring normal mode descriptions from one molecule to another, structurally similar molecule.
Each normal mode is treated as a column vector of dimension 3N. The vectors which describe the normal modes of one molecule are used as a basis set to describe the normal modes of another, similar molecule. A dot product is calculated between each of the normal modes of the basis molecule with those of the other. Because the modes are normalized, the resulting dot product defines the percentage similarity between any two vibrations.
ViPA is currently dimensioned to work with molecules containing 100 atoms or less, but there is no theoretical limit on the size of the molecules on which vector projection analysis could be used. The molecules being compared must be reasonably similar, i.e. one molecule should be a simple perturbation of the other, as in the case of isotopic substitutions, a change in electronic state, or, for instance, a change in chemical substituents.
ViPA can be used to perform stand-alone isotopic substitution calculations, or to perform rotational reorientations of input molecules. The program also provides output files containing the normal modes suitable for viewing in the program XMOL .
Usually less than one minute of computer time is required to execute ViPA, depending on the size of the molecules being compared.
|||E.B. Wilson, J.C. Decius, and P.C. Cross. Molecular Vibrations. (New York: Dover Publications, Inc., 1980).|
|||XMOL, Minneapolis, MN: Minnesota Supercomputer Center, Inc., (1993).|
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