Docking with Autodock and Molecular Dynamic analysis with Gromacs: Part of Indonesian Herbal Farmacological activities screening in Silico 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, Faculty of Computer Science, Universitas Indonesia Supported by The Indonesian Ministry of Research and Technology Office, 2009-2010,research grant

Gromacs

  GROMACS is a versatile package program to perform molecular dynamics.

GROMACS can be run with single processor or using multiple processor (parallel using standard MPI communication)  Our Research is study the performance (time) between, on the Cluster computing resources and on the GPU (Graphic Processor Unit)

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.

Hardware Specification

   Head node  Sun Fire X2100   AMD Opteron 2 GB RAM 2.2GHz (Dual Core)  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

GPU Engine Specs: Memory Specs: Feature Support:

GPU 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 CUDA Cores Graphics Clock (MHz) Processor Clock (MHz) Texture Fill Rate (billion/sec) Memory Clock (MHz) Standard Memory Config Memory Interface Width Memory Bandwidth (GB/sec)

128 738 MHz 1836 MHz 47.2

1100 512MB or 1 GB GDDR3 256-bit 70.4

File Preparation

File Cyp34a

Convert File Into .topology & .gro

pdb2gmx -f 1TQN.pdb -p 1TQN.top -o 1TQN.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 –o 1TQN-solvate.pdb

Energy Minimization grompp -np 16 -f md.mdp -c 1TQN.gro -p 1TQN.top -o 1TQN-md.tpr

1TQN-md.tpr is ready to be executed with 16 processor

Md-job.sh

#!/bin/sh # CYP34A #$ -N gromacs #$ -cwd # Jumlah prosesor #$ -pe mpich 16 #$ -l arch=lx24-x86 #$ -o /export/home/nico/cyp3a4/stdout #$ -e /export/home/nico/cyp3a4/stderr #$ -i /export/home/nico/cyp3a4/stdin # # needs in # $NSLOTS # the number of tasks to be used # $TMPDIR/machines # a valid machine file to be passed to mpirun echo "Got $NSLOTS slots." /usr/bin/mpirun -np $NSLOTS -machinefile $TMPDIR/machines /export/home/nico/gromacs/bin/mdrun_mpi -s /export/home/nico/cyp3a4/1TQN -md.tpr -o /export/home/nico/cyp3a4/1TQN -md.trr -c /export/home/nico/cyp3a4/1TQN -after-md.gro -np 16 -v

qsub md-job.sh

File Cyp34a (GPU)

Convert File Into .topology & .gro

pdb2gmx -f 1TQN.pdb -p 1TQN.top -o 1TQN.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 –o 1TQN-solvate.pdb

Energy Minimization grompp -f md.mdp -c 1TQN.gro -p 1TQN.top -o 1TQN-md.tpr

Production Simulation mdrun-openmm -v -deffnm 1TQN-md

File Curcumin

topol.tpr is ready to be executed with 10 processor grompp -np 10 -f md.mdp -c lox_pr.gro -p model.top -o topol.tpr

dt x nsteps = …pikosecond 0.002 x 100000 = 200 pikosecond

Md-job.sh

#!/bin/sh # Curcumin #$ -N gromacs #$ -cwd # Jumlah prosesor #$ -pe mpich 10 #$ -l arch=lx24-x86 #$ -o /export/home/ari/simulasi/curcumin10/stdout #$ -e /export/home/ari/simulasi/curcumin10/stderr #$ -i /export/home/ari/simulasi/curcumin10/stdin # # needs in # $NSLOTS # the number of tasks to be used # $TMPDIR/machines # a valid machine file to be passed to mpirun echo "Got $NSLOTS slots." /usr/bin/mpirun -np $NSLOTS -machinefile $TMPDIR/machines /export/home/nico/gromacs/bin/mdrun_mpi -s /export/home/ari/simulasi/curcumin12/topol.tpr -o /export/home/ari/simulasi/curcumin12/curcumin12.trr -c /export/home/ari/simulasi/curcumin12/lox_pr.gro -np 10 –v

qsub md-job.sh

File Curcumin (GPU)

grompp -f md.mdp -c lox_pr.gro -p model.top -o curcumin.tpr

dt x nsteps = …pikosecond 0.002 x 100000 = 200 pikosecond Production Simulation mdrun-openmm -v -deffnm curcumin

Performance Result

File : Curcumin

Single Processsor GPU (GTS 250) GPU (GTS 250)

Performance Time

24h:01M 17h:01M 9h:24m

Timesteps

200 ps 200 ps 100 ps

File : CYP3A4

Single Processsor GPU (GTS 250) GPU (GTS 250)

Performance Time

22h :32 M 14h : 23M 7h : 45 M

Timesteps

200 ps 200 ps 100 ps