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AutoDock for GPUs using OpenCL
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README.md

AutoDock-GPU: AutoDock for GPUs using OpenCL

Features

  • OpenCL-accelerated version of AutoDock4.2.6. It leverages the embarrasingly parallelism of its LGA by processing ligand-receptor poses in parallel over multiple compute units.
  • Besides the legacy Solis-Wets local search method, AutoDock-GPU adds newly implemented local-search methods based on gradients of the scoring function. One of these methods, ADADELTA, has proven to increase significantly the docking quality in terms of RMSDs and scores.
  • It targets platforms based on GPU as well as multicore CPU accelerators.
  • Observed speedups of up to 4x (quad-core CPU) and 56x (GPU) over the original serial AutoDock 4.2 (Solis-Wets) on CPU.

Setup

Operating system: Linux CPU GPU
CentOS 6.7 & 6.8 / Ubuntu 14.04 & 16.04 Intel SDK for OpenCL 2017 AMD APP SDK v3.0 / CUDA v8.0 & v9.0

Other environments or configurations likely work as well, but are untested.

Compilation

make DEVICE=<TYPE> NUMWI=<NWI>
Parameters Description Values
<TYPE> Accelerator chosen CPU, GPU
<NWI> OpenCL work-group size 16, 32, 64, 128, 256

After successful compilation, the host binary autodock_<type>_<N>wi is placed under bin.

Binary-name portion Description Values
<type> Accelerator chosen cpu, gpu
<N> OpenCL work-group size 16, 32, 64, 128, 256

Usage

Basic command

./bin/autodock_<type>_<N>wi \
-ffile <protein>.maps.fld \
-lfile <ligand>.pdbqt \
-nrun <nruns>
Mandatory options Description Value
-ffile Protein file <protein>.maps.fld
-lfile Ligand file <ligand>.pdbqt

Example

./bin/autodock_gpu_64wi \
-ffile ./input/1stp/derived/1stp_protein.maps.fld \
-lfile ./input/1stp/derived/1stp_ligand.pdbqt \
-nrun 10

By default the output log file is written in the current working folder. Examples of output logs can be found under examples/output.

Supported arguments

Argument Description Default value
-nrun # LGA runs 1
-nev # Score evaluations (max.) per LGA run 2500000
-ngen # Generations (max.) per LGA run 27000
-lsmet Local-search method sw (Solis-Wets)
-lsit # Local-search iterations (max.) 300
-psize Population size 150
-mrat Mutation rate 2 (%)
-crat Crossover rate 80 (%)
-lsrat Local-search rate 6 (%)
-trat Tournament (selection) rate 60 (%)
-resnam Name for docking output log "docking"
-hsym Handle symmetry in RMSD calc. 1

For a complete list of available arguments and their default values, check getparameters.cpp.

Documentation

Visit the project Wiki.

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