![]() #Animate secondary structure vmd plus#The huge amount of data generated by various MD applications plus their demands for a high-performance and energy-efficient storage system put a tremendous pressure on traditional rotation-based hard disk drives (HDDs). In addition to holding raw data for CPUs to solve various computational problems, extra storage is needed to accommodate processed data and intermediate data from separate computational steps. For example, data collected at the European Molecular Biology Laboratory require a storage capacity of 160 PB as of late 2018. ![]() These applications normally generate a huge amount of simulation data for a visualization tool like VMD to visualize and analyze. MD applications span a wide range of scientific domains, from VASP for chemical materials, XcrySDen for crystallines, to NAMD for computing and structural biology. It has been widely adopted by numerous molecular dynamics (MD) applications as a graphical front end for rendering and animating molecule undergoing simulations on a remote computer. Visual molecular dynamics (VMD) is a popular molecular graphics program designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, and lipid bilayer assemblies. Besides, ADA allows the 1TB memory server to render more than 2x the VMD graphs while cutting energy consumption by 3x. Our experimental results show that compared to a traditional file system an ADA-assisted file system improves data processing turnaround time by up to 13.4x and reduces memory usage for data rendering by up to 2.5x. Further, we evaluate ADA by running a computational biology application on the three platforms. ![]() Next, we implement an ADA prototype, which is then integrated into three computing platforms: an SSD server, a nine-node OrangeFS storage cluster, and a fat-node server with 1 TB memory. It provides host CPUs with only the data needed instead of an entire raw dataset. To solve it, we propose ADA (application-conscious data acquirer), a light-weight file system middleware that can perform an application-conscious data pre-processing. #Animate secondary structure vmd how to#One challenge faced by domain scientists, however, is how to filter out inactive data (i.e., data irrelevant to the subject) from the enormous output of an MD simulation. Visual molecular dynamics (VMD) has been widely used by numerous molecular dynamics (MD) applications to animate and analyze the trajectory of an MD simulation. ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |