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Gromacs

Molecular Dynamic analysis with Gromacs: Part of Indonesian Herbal Farmacological activities screening in Silico study On a Cluster computing environment.

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Gromacs

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  1. Molecular Dynamic analysis with Gromacs: Part of Indonesian Herbal Farmacological activities screening in Silico study On a Cluster computing environment. Screening aktifitas farmakologis beberapa bahan aktif tumbuhan obat Indonesia secara in silico menggunakan High Performance Computing berbasis Cluster system Joint research : Arry Yanuar, Dept of Pharmacy, and Heru Suhartanto, Ari Wibisono, Faculty of Computer Science, Universitas Indonesia Supported by The Indonesian Ministry of Research and Technology Office, 2009-2010,research grant

  2. Gromacs • GROMACS is a one of the best program to perform molecular dynamics for protein and bio-molecule simulation. • GROMACS can be run with single processor or using multiple processor (parallel using standard MPI communication) • Our Research is to study the performance (time) between, on the Cluster computing resources and on the GPU (Graphic Processor Unit)

  3. The InGrid: http://grid.ui.ac.id Let’s see a 1 minute visit to the portal and the monitor

  4. Hastinapura • Hastinapura.grid.ui.ac.id is the first Cluster computing resources, the Faculty of Computer Science Universitas Indonesia. •  This cluster can be used to run parallel and serial applications (gromacs). •  It consists of 16 dual-core machines that act as worker nodes.

  5. Hardware Specification • Head node • Sun Fire X2100 • AMD Opteron 2.2GHz (Dual Core) • 2 GB RAM • Debian GNU/Linux 3.1 “Sarge” • Worker nodes (16) • Sun Fire X2100 • AMD Opteron 2.2GHz (Dual Core) • 1 GB RAM • Debian GNU/Linux 3.1 “Sarge” • Storage node • Dual Intel Xeon 2.8GHz (HT) • 2 GB RAM • Debian GNU/Linux 4.0-testing “Etch” • Harddisk 3x320 GB

  6. GPU Engine Specs: Memory Specs: Feature Support: GPU PC Hardware Specification • Dual Core 3.2 GHz • 4 GB RAM • Ubuntu 9.04 64 Bit • Harddisk 80 Gb • Gromacs 4.05 + OpenMM • GeForce GTS 250

  7. File Preparation

  8. File Cyp34a Convert File Into .topology & .gro Periodic Boundary Condition editconf -f 1TQN.gro -o 1TQN.gro -d 1.0 Adding solvent into the molecule genbox -cp 1TQN.gro -cs spc216.gro -p 1TQN.top –o1TQN-solvate.pdb Energy Minimization 1TQN-md.tpr is ready to be executed with 16 processor

  9. Md-job.sh

  10. File Cyp34a (GPU) Convert File Into .topology & .gro Periodic Boundary Condition editconf -f 1TQN.gro -o 1TQN.gro -d 1.0 Adding solvent into the molecule genbox -cp 1TQN.gro -cs spc216.gro -p 1TQN.top –o1TQN-solvate.pdb Energy Minimization Production Simulation

  11. File Curcumin topol.tpr is ready to be executed with 10 processor dt x nsteps = …pikosecond 0.002 x 100000 = 200 pikosecond

  12. Md-job.sh

  13. File Curcumin (GPU) dt x nsteps = …pikosecond 0.002 x 100000 = 200 pikosecond Production Simulation

  14. Performance Result CYP3A4 Result on InGrid is almost the same with the above result

  15. The next targets: Improve the performance Thank you !

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