VinaLC

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Description

A very popular PC-based molecular docking program, AutoDock Vina, was modified and parallelized, using an MPI and multithreading hybrid scheme, and potentially can be used in the future on exascale machines, without sacrificing accuracy. The resulting program scales up to more than 15K CPUs with a very low overhead cost.

Reference

Xiaohua Zhang, Sergio E. Wong, and Felice C. Lightstone. (2013) Message Passing Interface and Multithreading Hybrid for Parallel Molecular Docking of Large Databases on Petascale High Performance Computing Machines. J. Comput. Chem. 34, 915-927. http://onlinelibrary.wiley.com/doi/10.1002/jcc.23214/abstract

Availability

VinaLC version: 1.1.2

Use

module add vinalc-1.1.2
vinalc

Documentation

http://mvirdb1.llnl.gov/static_catsid/vina/usersGuide.html

Licence

Apache License 2.0

Supported platforms

Linux

Program administrator

meta@cesnet.cz

Homepage

http://mvirdb1.llnl.gov/static_catsid/vina/index.html

Usage

Sample of usage:

module add vinalc-1.1.2
cd /storage/brno6/home/aqua/vstupy/
mpirun --mca btl ^openib vinalc --recList /storage/brno6/home/vstupy/ligands/receptor_rigid.txt --fleList /storage/brno6/home/aqua/vstupy/ligands/receptor_flex.txt --ligList /storage/brno6/home/aqua/vstupy/ligands/ligands.txt --geoList /storage/brno6/home/aqua/vstupy/ligands/conf-4ey7.txtx > vinalcOutput