UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales.

Abstract

The UNRES package for coarse-grained simulations, which has recently been optimized to treat large protein systems, has been implemented on Graphical Processor Units. An over 100-time speed up of the GPU code (run on an NVIDIA A100) with respect to the sequential code and an 8.5 speed-up with respect to the parallel (OpenMP) code (run on 32 cores of 2 AMD EPYC 7313 CPUs) has been achieved for large proteins (with size over 10,000 residues). Due to the averaging over the fine-grain degrees of freedom, 1 time unit of UNRES simulations is equivalent to about 1,000 time units of laboratory time, therefore millisecond time scale of large protein systems can be reached with the UNRES-GPU code. The complete source code of UNRES-GPU can be downloaded from https://projects.task.gda.pl/eurohpcpl-public/unres. Supplementary data are available at Bioinformatics online.