摘要
ABEEMσπ/MM模型程序中,计算静电相互作用能非常耗费机时.针对原串行程序中多个循环相互嵌套的求解部分,进行循环带状划分并行化处理.经测试表明,利用新编制的并行程序进行动力学模拟,并行加速比以线性趋势提高、求解静电相互作用能速度大幅度加快、尤其是针对原子数较多的分子体系效果比较理想.利用36个CPU,对于位点数为10 000左右的蛋白质体系,进行1ns的动力学模拟,至少可以节省1年左右的时间,明显地提高了研究蛋白质体系性质的效率.
In ABEEMσπ/MM method,the program of calculating the electrostatic interaction energy is very time-consuming.Considering several nesting circular parts of serial program,this paper develops a cyclic-striped partitioning parallel method.The tested results show that parallel speedup increased with linear trend,the speed of the calculation has obviously increased in dynamics simulation by this new compiled parallel program,especially on a macromolecular system.Using 36 CPUs,for the protein system with about 10000 sites,we can save at least one year for 1ns dynamics simulation.The new program has obviously increased the efficiency of the properties of protein systems.
出处
《辽宁师范大学学报（自然科学版）》
CAS
2009年第4期457-461,共5页
Journal of Liaoning Normal University:Natural Science Edition
基金
国家自然科学基金项目(20633050)
