ISSN:
0192-8651
Keywords:
Computational Chemistry and Molecular Modeling
;
Biochemistry
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Chemistry and Pharmacology
,
Computer Science
Notes:
An algorithm is presented within the context of the calculation of the time-relaxation behavior of the hydration shells around atomic sites in biomolecules. We report a calculation of the time-relaxation behavior of the first and second hydration shells of polar, hydrophobic, and charged groups in a protein, crambin. The water mean residence times around protein groups are obtained from averages over configurations sampled during a 325-ps molecular dynamics simulation of crambin in solution. A convolution arising in the calculation of the mean relaxation time is implemented using a parallel prefix operator. A new characterization is given of the parallel prefix operator as a linear transformation, and this formulation enables us to derive efficient factorization of the convolution as a product of two parallel prefix operations. The parallel prefix operations are implemented in logarithmic time. © John Wiley & Sons, Inc.
Additional Material:
2 Ill.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1002/jcc.540141116
