Vina-GPU-CUDA

A CUDA implementation of Vina-GPU

Note: this is a demo of CUDA Vina-GPU, cuda related files are in ./inc/cuda dir

Compilation on Linux

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.

1. install boost library (current version is 1.77.0)

2. install CUDA Toolkit (current version is 11.5) if you are using NVIDIA GPU cards

3. set the BOOST_LIB_PATH in Makefile according to the boost library installation path

4. 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)

5. set NVCC_COMPILER according to the nvcc compiler installatio path. Some options are given below:

6. type make clean and make cuda to build Vina-GPU

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

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

Usage

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