title: Modified Anderson Method for Accelerating 3D-RISM Calculations Using Graphics Processing Unit.
abstract: A fast algorithm is proposed to solve the three-dimensional reference interaction site model (3D-RISM) theory on a graphics processing unit (GPU). 3D-RISM theory is a powerful tool for investigating biomolecular processes in solution; however, such calculations are often both memory-intensive and time-consuming. We sought to accelerate these calculations using GPUs, but to work around the problem of limited memory size in GPUs, we modified the less memory-intensive "Anderson method" to give faster convergence to 3D-RISM calculations. Using this method on a Tesla C2070 GPU, we reduced the total computational time by a factor of 8, 1.4 times by the modified Andersen method and 5.7 times by GPU, compared to calculations on an Intel Xeon machine (eight cores, 3.33 GHz) with the conventional method.
authors.affiliation: Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Maruyama
authors.affiliation: Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585, Japan.|Department of Functional Molecular Science, The Graduate University for Advanced Studies, Okazaki 444-8585, Japan.
authors.forename: Fumio
authors.initials: F
authors.lastname: Hirata