Parallelize The Program Of Energy In ABEEMσπ/MM Method

This thesis is mainly divided into two parts:first, by analysising each part of serial process multiple loop nested within of ABEEMσπforce field model to calculate the electrostatic interaction term, provide the parallel processing program of loop ribbon division, iterative solution; second, the above method is applied to ABEEMσπforce field model to solve all the other energy terms of the serial program, implemented ABEEMσπforce field model to solve the energy of all the items parallel.With the high-speed development of computer, calculation methods and engineering applications, solving problems of complexity and the capacity has been increased, almost all science are on the road of quantification and definition. While the original serial algorithm can not meet the current requirements of calculation, making serial computer could not do. Cluster, represented by MPI (Message Passing Interface) parallel computer system for solving large numerical problems become the main platform. Resulting in a number of emerging branches of computer science, such as computational physics, computational mechanics. computational chemistry and computational materials science. Computational Science has been parallel with the traditional theoretical and experimental scientific, which was as the third scientific method and widely used in weather forecasting, oil exploration, transportation, aerospace and other major engineering fields.ABEEMσπmodel to calculate the electrostatic interaction energy system, that including all the atoms in demand system,σbond, lone pairs,πbond electrostatic interaction between sites combined. Electrostatic interaction energy of the original program requirements by serial number of each nested loop in turn calculated to achieve, this method for solving electrostatic interaction of biological macromolecules can take a long time, so that decreased the efficiency of research questions. This solution uses belt loop, iterative solution of the parallel distribution processing program, making the serial program of the electrostatic interaction energy running on the parallel MPI environment with multi-machine parallel programs. The new procedure considerably reduced the machine time, and get consistent results with the serial. Subsequently, the paper has used this method to solve the other energy items of ABEEMσπforce field model program. And using 10 different systems to perform modeling molecular dynamics simulations for testing of theim.The tested results show that parallel speedup increased with linear trend, the speed of calculation has obviously increased in dynamics simulation by this new compiled parallel program, especially on a macromolecular system.