3 Publications

3.1 Papers

3.1.6 Chronological list

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3.1.6.34 Totrov, M.M., and Abagyan, R.A. (1994). Efficient parallelization of the energy, surface and derivative calculations for internal coordinate mechanics. J. Comp. Chem., 15, 1105-1112

An efficient algorithm for parallelization of a molecular mechanics program operation in the space of internal coordinates such as dihedral angles, bond angles, and bond length, is described. The iterative procedure to calculate analytical energy derivatives with respect to the internal coordinates was modified to allow parallelization. Computationally intensive modules that calculate energy and its derivatives, solvent-accessible surface, electrostatic polarization energy and that update lists of interactions were parallelized with nearly 100% efficiency. The proposed strategy for the shared-memory computer architecture is easily scalable and requires minimum changes in a program code. The overall speedup for a realistic calculation minimizing the energy of a myoglobin reaches a factor of 3 for 4 processors.