AutoDock-GPU: AutoDock for GPUs using OpenCL

Features

• OpenCL-accelerated version of AutoDock4.2.6. It leverages its embarrasingly parallelizable 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	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
macOS Catalina 10.15.1	Apple / Intel	Apple / Intel Iris, Radeon Vega 64

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	1, 2, 4, 8, 16, 32, 64, 128, 256

Hints: The best work-group size depends on the GPU and workload. Try NUMWI=128 or NUMWI=64 for modern cards with the example workloads. On macOS, use NUMWI=1 for CPUs.

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	1, 2, 4, 8,16, 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	80 (%)
-trat	Tournament (selection) rate	60 (%)
-resnam	Name for docking output log	"docking"
-hsym	Handle symmetry in RMSD calc.	1
-devnum	OpenCL device number	1
-cgmaps	Use individual maps for CG-G0 instead of the same one	0 (use same map)

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

Documentation

Visit the project Wiki.