Open-architecture Implementation of Fragment Molecular Orbital Method for Peta-scale Computing

Large-Scale MP2 Calculations on the Blue Gene Architecture Using the Fragment Molecular Orbital Method.

Benchmark timings are presented for the fragment molecular orbital method on a Blue Gene/P computer. Algorithmic modifications that lead to enhanced performance on the Blue Gene/P architecture include strategies for the storage of fragment density matrices by process subgroups in the global address space. The computation of the atomic forces for a system with more than 3000 atoms and 44 000 bas...

ppOpen-HPC: Open Source Infrastructure for Development and Execution of Large-Scale Scientific Applications on Post-Peta-Scale Supercomputers with Automatic Tuning (AT)

We propose an open source infrastructure for development and execution of optimized and reliable simulation codes on post-petascale (pp) parallel computers with heterogeneous computing nodes which consist of multicore CPU’s and accelerators., named “ppOpen-HPC”. ppOpen-HPC consists of various types of libraries, which covers various types of procedures for scientific computations. Source code d...

Large-Scale Electronic-State Calculations of Protein- Ligand Systems for Drug Design with Fragment Molecular Orbital Method

Available online at www.prace-ri.eu Partnership for Advanced Computing in Europe Implementation of Fragment Orbital Method (FMO) for Highly Parallelized Quantum Chemical Calculations with CP2K

The reported work aims at implementation of a method allowing realistic simulation of large or extra-large biochemical systems (of 10 to 10 atoms) with first-principle quantum chemical methods. The current methods treat the whole system simultaneously. In this way the comput time increases rapidly with the size of the system and does not allow efficient parallelization of the calculations due t...

Geometry optimizations of open-shell systems with the fragment molecular orbital method.

The ability to perform geometry optimizations on large molecular systems is desirable for both closed- and open-shell species. In this work, the restricted open-shell Hartree-Fock (ROHF) gradients for the fragment molecular orbital (FMO) method are presented. The accuracy of the gradients is tested, and the ability of the method to reproduce adiabatic excitation energies is also investigated. T...