Docking with Autodock and Molecular Dynamic analysis with Gromacs: Part of Indonesian Herbal Farmacological activities screening in Silico

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2 Δεκ 2013 (πριν από 4 χρόνια και 29 μέρες)

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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


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

128

Graphics Clock (MHz)

738

MHz

Processor Clock (MHz)

1836

MHz

Texture Fill Rate
(billion/sec)

47.2


Memory Clock (MHz)

1100


Standard Memory Config

512MB or 1

GB

GDDR3

Memory Interface Width

256
-
bit

Memory Bandwidth
(GB/sec)

70.4

GPU Engine Specs:

Memory Specs:

Feature Support:

File Preparation

File Cyp34a

pdb2gmx
-
f 1TQN.pdb
-
p 1TQN.top
-
o 1TQN.gro

editconf
-
f 1TQN.gro
-
o 1TQN.gro
-
d 1.0

genbox
-
cp 1TQN.gro
-
cs spc216.gro
-
p 1TQN.top

o

1TQN
-
solvate.
pdb

grompp
-
np
16

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

Convert File Into .topology & .gro

Periodic Boundary Condition

Adding solvent into the molecule

Energy Minimization

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

#!/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

Md
-
job.sh

qsub

md
-
job.sh

File Cyp34a (GPU)

pdb2gmx
-
f 1TQN.pdb
-
p 1TQN.top
-
o 1TQN.gro

editconf
-
f 1TQN.gro
-
o 1TQN.gro
-
d 1.0

genbox
-
cp 1TQN.gro
-
cs spc216.gro
-
p 1TQN.top

o

1TQN
-
solvate.
pdb

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

Convert File Into .topology & .gro

Periodic Boundary Condition

Adding solvent into the molecule

Energy Minimization

m
drun
-
openmm

-
v
-
deffnm 1TQN
-
md

Production Simulation

File
Curcumin

grompp
-
np
10

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

topol.tpr is ready
to be executed
with 10 processor

dt

x
nsteps

= …
pikosecond

0.002 x 100000 = 200
pikosecond


Md
-
job.sh

#!/bin/sh

#
Curcumin

#$
-
N gromacs

#$
-
cwd

# Jumlah prosesor

#$
-
pe mpich
1
0

#$
-
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


m
drun
-
openmm

-
v
-
deffnm
curcumin

Production Simulation

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