Calculating the electrostatic potential of molecular models with separate evaluations by conventional, vector, and array processors

A simple computational scheme for estimating the electrostatic potential about molecular models of moderate size is given. The large amount of calculations required for the evaluation of the hypersurface lends itself to treatment by high speed, unconventional computing machines. The essence of these calculations lies in Coulombic interactions that are computed between hypothetical proton test probes positioned in a gridded region surrounding the model and the partial electrostatic charges (CNDO/2) of each atom in the model. A specific scientific application is discussed which involves the recognition of amino acids and nucleotide bases. Three different evaluations of the potential hypersurface within the context of this approach were made. The first was performed on a VAX 11/780 which is a general purpose machine widely used in the scientific community; the second was performed using a pipelined Vector Processor, the FPS AP-120B; and the third by a processor array, the ILLIAC-IV. A comparison of the architectures and processing speeds of each class of machines is made. The computing power observed is consistent with the design and purpose of each machine. Also discussed are methods for displaying the vast amount of data that result from such calculations. It is determined that computer graphics offers an effective means for extracting information from large amounts of data. Finally, the scientific value of the calculations are briefly discussed. If caution is applied to interpreting the results, then the electrostatic potential (EP) mappings can be useful in identifying sites of potential chemical interactions.