Benchmarking on Publicly Available Philippine Computational Resources

NAMD benchmarks were done on five different proteins with varying system sizes (anoplin, kalata B1, North-Atlantic ocean pout antifreeze protein, Pseudomonas aeruginosa PAO1 lipase and octopamine receptor in mushroom bodies, OAMB) solvated with TIP3P water through four different publicly available computer resources in the Philippines. Our results show that the high-end desktop generated the most ns/day for small and medium-sized systems (e.g. anoplin, kalata B1, and antifreeze protein) while BlueGene/P generated the most ns/day for larger system sizes (e.g. lipase and octopamine receptor). Although these computing resources are capable of exploring protein behavior through molecular dynamics (MD) simulations for small to medium-sized systems, dealing with large systems require tremendous computational resources. This benchmark highlights the importance of intercommunication in NAMD. Moreover, our results showed the advantage of using GPU-accelerated desktops for certain MD simulations. However, the poor scalability of the high-end desktop does not make it viable for simulating large systems. Improvements in Philippine computing infrastructure and protocol is highly recommended to keep up with advances in high performance computing globally. This work is supported in part by the Newton Agham Programme (Project Number FP160010), the Office of the Vice Chancellor for Research and Development (Grant Number PNE151512), the Natural Sciences Research Institute, and the Office of the Vice President for Academic Affairs of the University of the Philippines Diliman under the Emerging Interdisciplinary Research (EIDR) Program. Acknowledgment is also made to ASTI and the Computing and Archiving Research Environment (CoARE) of the Department of Science and Technology, Philippines, Computational Science Research Center and Philippine Genome Center Core Facility for Bioinformatics of the University of the Philippines for the allocation of computing resources required for this study. Ronny L. Cheng is affiliated with the Institute of Chemistry, University of the Philippines, Diliman, Quezon City, Philippines (e-mail: rlcheng@up.edu.ph). Ren Tristan A. dela Cruz is affiliated with the Department of Computer Science, University of the Philippines, Diliman, Quezon City, Philippines (e-mail: rentristandelacruz@gmail.com) Francoise Neil D. Dacanay is affiliated with the Institute of Chemistry, University of the Philippines, Diliman, Quezon City, Philippines (e-mail: fddacanay@upd.edu.ph). Gil C. Claudio is affiliated with the Institute of Chemistry, University of the Philippines, Diliman, Quezon City, Philippines (e-mail: gcc.upd@gmail.com). Ricky B. Nellas is affiliated with the Institute of Chemistry, University of the Philippines, Diliman, Quezon City, Philippines (e-mail: ricky.nellas@upd.edu.ph).