1994/10/01 by Maxim Totrov, Ruben Abagyan · 1 citation
Biochemistry, Genetics and Molecular Biology · Materials Science · Physics and Astronomy · #Protein Structure and Dynamics #Enzyme Structure and Function #Advanced Chemical Physics Studies
paper · doi:10.1002/jcc.540151006
openalex publication_date 1994/10/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/05/21
Abstract An efficient algorithm for parallelization of a molecular mechanics program operating in the space of internal coordinates such as dihedral angles, bond angles, and bond lengths 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. © 1994 by John Wiley & Sons, Inc.