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 2.2GHz (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
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)
128
738 MHz
1836 MHz
Memory Clock (MHz)
Standard Memory Config
Memory Interface Width
Memory Bandwidth
(GB/sec)
1100
512MB or 1 GB GDDR3
256-bit
47.2
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
qsub md-job.sh
#
# 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 $TMPDIR/machines
/export/home/nico/gromacs/bin/mdrun_mpi
-s /export/home/nico/cyp3a4/1TQN -md.tpr
-o /export/home/nico/cyp3a4/1TQN -md.trr
-c /export/home/nico/cyp3a4/1TQN -after-md.gro
-np 16 -v
File Cyp34a (GPU)
Convert File Into .topology & .gro
pdb2gmx -f 1TQN.pdb -p 1TQN.top -o 1TQN.gro
Periodic Boundary Condition
editconf -f 1TQN.gro -o 1TQN.gro -d 1.0
Adding solvent into the molecule
genbox -cp 1TQN.gro -cs spc216.gro -p 1TQN.top –o
1TQN-solvate.pdb
Energy Minimization
grompp -f md.mdp -c 1TQN.gro -p 1TQN.top -o 1TQN-md.tpr
Production Simulation
mdrun-openmm -v -deffnm 1TQN-md
File Curcumin
topol.tpr is ready
to be executed
with 10 processor
grompp -np 10 -f md.mdp -c lox_pr.gro -p model.top -o topol.tpr
dt x nsteps = …pikosecond
0.002 x 100000 = 200 pikosecond
Md-job.sh
#!/bin/sh
# Curcumin
#$ -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
Performance
Time
Timesteps
Single
Processsor
24h:01M
200 ps
GPU (GTS 250)
17h:01M
200 ps
GPU (GTS 250)
9h:24m
100 ps
File : CYP3A4
Performance
Time
Timesteps
Single
Processsor
22h :32 M
200 ps
GPU (GTS 250)
14h : 23M
200 ps
GPU (GTS 250)
7h : 45 M
100 ps