Vina-GPU+ further accelerates Vina-GPU and facilitates single receptor-multi-ligand docking.

Note: at least one GPU card is required and make sure the version of GPU driver is up to date.

1. For the first time to use Vina-GPU+, please run Vina-GPU+_K.exe with command ./Vina-GPU+_K.exe --config=./input_file_example/2bm2_config.txt You are supposed to have the docking results test_out file ,Kernel1_Opt.bin file and Kernel2_Opt.bin file
2. Once you have the Kernel1_Opt.bin file and Kernel2_Opt.bin file, you can run Vina-GPU+.exe without compiling the kernel files (thus to save more runtime)

When you run Vina-GPU+.exe, please make sure Kernel1_Opt.bin file and Kernel2_Opt.bin file are in the same directory

For the usage and limitaiton of Vina-GPU+, please check Usage and Limitation. A graphic user interface (GUI) is also provided for Windows users, please check GUI

Visual Studio 2019 is recommended for build Vina-GPU from source

1. install boost library (current version is 1.77.0)

2. install CUDA Toolkit (current version is v11.5) if you are using NVIDIA GPU cards

   Note: the OpenCL library can be found in CUDA installation path for NVIDIA or in the driver installation path for AMD

3. add ./lib ./OpenCL/inc $(YOUR_BOOST_LIBRARY_PATH) $(YOUR_BOOST_LIBRARY_PATH)/boost $(YOUR_CUDA_TOOLKIT_LIBRARY_PATH)/CUDA/v11.5/include in the include directories

4. add $(YOUR_BOOST_LIBRARY_PATH)/stage/lib $(YOUR_CUDA_TOOLKIT_PATH)/CUDA/lib/x64in the addtional library

5. add OpenCL.lib in the additional dependencies

6. add --config=./input_file_example/2bm2_config.txt in the command arguments

7. add NVIDIA_PLATFORM OPENCL_3_0 WINDOWS in the preprocessor definitions if necessary

8. if you want to compile the binary kernel file on the fly, add BUILD_KERNEL_FROM_SOURCE in the preprocessor definitions

9. build & run Note: ensure the line ending are CLRF

Note: At least 8M stack size is needed. To change the stack size, use ulimit -s 8192.

1. install boost library (current version is 1.77.0)

2. install CUDA Toolkit (current version is v11.5) if you are using NVIDIA GPU cards

   Note: OpenCL library can be usually in /usr/local/cuda (for NVIDIA GPU cards)

3. change the BOOST_LIB_PATH and OPENCL_LIB_PATH accordingly in Makefile

4. set GPU platform GPU_PLATFORM and OpenCL version OPENCL_VERSION in Makefile. some options are given below:

   Note: -DOPENCL_3_0 is highly recommended in Linux, please avoid using -OPENCL_1_2 in the Makefile setting. To check the OpenCL version on a given platform, use clinfo.

   Macros	Options	Descriptions
   GPU_PLATFORM	-DNVIDIA_PLATFORM / -DAMD_PLATFORM	NVIDIA / AMD GPU platform
   OPENCL_VERSION	-DOPENCL_3_0 / -OPENCL_2_0	OpenCL version 3.0 / 2.0

5. type make clean and make source to build Vina-GPU+ that compile the kernel files on the fly (this would take some time at the first use)

6. after a successful compiling, Vina-GPU+ can be seen in the directory

7. type ./Vina-GPU+ --config ./input_file_example/2bm2_config.txt to run Vina-GPU+

8. once you successfully run Vina-GPU+, its runtime can be further reduced by typing make clean and make to build it without compiling kernel files (but make sure the Kernel1_Opt.bin file and Kernel2_Opt.bin file is unchanged)

9. other compile options: