Artikel Jurnal :: Kembali

Artikel Jurnal :: Kembali

Judul Performance Analysis of Molecular Dynamics Simulation of PfENR Enzyme using AMBER on Cluster and GPU computing environment
Nomor Panggil MK-Pdf
Pengarang
Pengarang/kontributor lain
Subjek
Penerbitan 2014
Kata Kunci molecular dynamic simulation ·  ·
 Info Lainnya
ISBN/ISSNnone
Deskripsi Fisiknone
Catatan Seri none
Catatan Umumnone
Lokasinone
VolumeVolume 6, Number 1, January 2014
  • Ketersediaan
  • File Digital: 1
  • Ulasan
  • Sampul
  • Abstrak
  • Tampilan MARC
Nomor Panggil No. Barkod Ketersediaan
MK-Pdf 03-17-105246953 TERSEDIA
Ulasan:
Tidak ada ulasan pada koleksi ini: 20461468
ABSTRACT
One of the processes requiring HPC environments is Molecular Dynamics ( MD ) . In tropical countries, the MD process is very important in the preparation of virtual screening experiments for anti-malaria search. Previous works on the virtual screening project for anti-malaria search conducted by WISDOM project uses grid infrastructure with 1,700 CPUs of various infrastructure provided in 15 countries [13]. In silico anti malaria compounds searching from Indonesian medical plants using virtual screening methods are urgently required. This can reduce the cost and time required compared to the direct searching or examining each compound by in vitro and in vivo which will spend a lot of time and expense . However, the use of thousands of processors is difficult for the researchers with limited resources in developing countries such as Indonesia.
Our of previous studies using MD with GROMACS shows the improvement of the simulation time using Cluster. But that is not the case for some of our previous works with AMBER on Cluster where we did not obtain significant speed up. However, our previous works running GROMACS on GPUs provided significant speed up about 12 times faster than that run on Cluster. In this study , we build a GPU -based computing environment and have some MD simulation with AMBER.
We used several computing environments such as cluster with 16 cores , GPU Geforce GTX 465 , GTX 470 , GTX 560 , GTX 680 , and GTX 780 . In addition to PfENR ( Plasmodium falciparum Enoyl acyl Carrier Protein Reductase ) enzyme , as benchmark we also conducted MD experiments on Myoglobin protein , Dihydrofolate reductase (DHFR) protein, and Ras - Raf protein . All experimental results showed that the slowest MD processes occurred on Cluster, followed in increasing order by GTX 560, GTX 465, GTX 470, GTX 680 and GTX 780. While the GPU speed up relative to cluster is about 24 , 26 , 32 , 24 , 77 and 101, respectively.
004
020
022
040LibUI eng rda
041eng
049[03-17-105246953]
053[03-17-105246953]
082
090MK-Pdf
100Heru Suhartanto, author
110
111
240
245|a Performance Analysis of Molecular Dynamics Simulation of PfENR Enzyme using AMBER on Cluster and GPU computing environment |c
246
250
260
260|a |b |c 2014
270
300
310
321
336text (rdacontent)
337computer (rdamedia)
338online resource (rdacarrier)
340
362
490
500
502
504
515
520ABSTRACT
One of the processes requiring HPC environments is Molecular Dynamics ( MD ) . In tropical countries, the MD process is very important in the preparation of virtual screening experiments for anti-malaria search. Previous works on the virtual screening project for anti-malaria search conducted by WISDOM project uses grid infrastructure with 1,700 CPUs of various infrastructure provided in 15 countries [13]. In silico anti malaria compounds searching from Indonesian medical plants using virtual screening methods are urgently required. This can reduce the cost and time required compared to the direct searching or examining each compound by in vitro and in vivo which will spend a lot of time and expense . However, the use of thousands of processors is difficult for the researchers with limited resources in developing countries such as Indonesia. Our of previous studies using MD with GROMACS shows the improvement of the simulation time using Cluster. But that is not the case for some of our previous works with AMBER on Cluster where we did not obtain significant speed up. However, our previous works running GROMACS on GPUs provided significant speed up about 12 times faster than that run on Cluster. In this study , we build a GPU -based computing environment and have some MD simulation with AMBER. We used several computing environments such as cluster with 16 cores , GPU Geforce GTX 465 , GTX 470 , GTX 560 , GTX 680 , and GTX 780 . In addition to PfENR ( Plasmodium falciparum Enoyl acyl Carrier Protein Reductase ) enzyme , as benchmark we also conducted MD experiments on Myoglobin protein , Dihydrofolate reductase (DHFR) protein, and Ras - Raf protein . All experimental results showed that the slowest MD processes occurred on Cluster, followed in increasing order by GTX 560, GTX 465, GTX 470, GTX 680 and GTX 780. While the GPU speed up relative to cluster is about 24 , 26 , 32 , 24 , 77 and 101, respectively.
533
534
536
546
590
650Molecular dynamics -- Computer simulation
653molecular dynamic simulation;
700Arry Yanuar, author; Alhadi Bustamam, author; Aruni Yasmin Azizah, author
710
711
850Universitas Indonesia
852Perpustakaan UI, Lantai 3
856
866
900
902
903[]