A CUDA implementation of Vina-GPU
Note: this is a demo of CUDA Vina-GPU, cuda related files are in ./inc/cuda dir
Environment: Ubuntu 18.04.6 LTS / nvcc version: 11.7 / NVIDIA-SMI 460.91.03 Driver Version: 460.91.03 CUDA Version: 11.2
Note: At least 8M stack size is needed. To change the stack size, use ulimit -s 8192.
install boost library (current version is 1.77.0)
install CUDA Toolkit (current version is 11.5) if you are using NVIDIA GPU cards
set the BOOST_LIB_PATH in Makefile according to the boost library installation path
set GRID_DIM according to the costumed grid size. Note: the value of GRID_DIM1GRID_DIM2 (eg. 64128) must equal to the value of thread(eg. 8192) parameter(see Usage)
set NVCC_COMPILER according to the nvcc compiler installatio path. Some options are given below:
type make clean and make cuda to build Vina-GPU
after a successful compiling, Vina-GPU can be seen in the directory
type ./Vina-GPU --config ./input_file_example/2bm2_config.txt to run Vina-GPU
| Arguments | Description | Default value |
|---|---|---|
| --config | the config file (in .txt format) that contains all the following arguments for the convenience of use | no default |
| --receptor | the recrptor file (in .pdbqt format) | no default |
| --ligand | the ligand file (in .pdbqt fotmat) | no default |
| --thread | the scale of parallelism (docking lanes) | 8192 |
| --search_depth | the number of searching iterations in each docking lane | heuristically determined |
| --center_x/y/z | the center of searching box in the receptor | no default |
| --size_x/y/z | the volume of the searching box | no default |