It has been shown that a small number of FPGAs can significantly accelerate certain computing tasks by up to two or three orders of magnitude. However, particularly intensive lar...
Arun Patel, Christopher A. Madill, Manuel Salda&nt...
The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle provide answers to some of the ...
David E. Shaw, Martin M. Deneroff, Ron O. Dror, Je...
Current high-performance applications are typically implemented on large-scale general-purpose distributed or multiprocessing systems often based on commodity microprocessors. Fie...
Navid Azizi, Ian Kuon, Aaron Egier, Ahmad Darabiha...
Background: We have developed the program PERMOL for semi-automated homology modeling of proteins. It is based on restrained molecular dynamics using a simulated annealing protoco...
Abstract: FPGA-based acceleration of molecular dynamics (MD) has been the subject of several recent studies. Implementing long-range forces, however, has only recently been address...