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change NUM_CORES

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2024-01-10 18:18:31 +08:00
parent a937bd0334
commit 660f741274
2 changed files with 10 additions and 3 deletions
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7
README.md
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@@ -9,3 +9,10 @@ micromamba create -n modeller modeller biopython pymol-open-source biopandas req
``` ```
modeller注册码：`MODELIRANJE`` modeller注册码：`MODELIRANJE``
## test
```shell
cp pdb_test/5isz.pdb pdb_gjm/
gmx_mpi pdb2gmx -f 5isz.pdb -o 5isz.gro -ff amber99sb-ildn -water tip3p -ignh -p topol.top
```

6
runner.py
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@@ -108,7 +108,7 @@ class SimulationRunner:
result = None result = None
# 保留1个核心不使用 # 保留1个核心不使用
num_cores = max(1, multiprocessing.cpu_count() - 1) # 避免核心数小于 1 num_cores = max(1, multiprocessing.cpu_count() - 1) # 避免核心数小于 1
os.environ['OMP_NUM_THREADS'] = str(num_cores) os.environ['NUM_CORES'] = str(num_cores)
try: try:
env_vars = { env_vars = {
"NAME": self.pdb_file.stem, "NAME": self.pdb_file.stem,
@@ -196,9 +196,9 @@ def main(simulation_steps, time_step, pdb_folder_path, bash_script_path, gmxrc_p
pool.join() pool.join()
if __name__ == "__main__": if __name__ == "__main__":
NSTEPS = 50000000 # Example: 50000000 steps NSTEPS = 50000 # Example: 50000000 steps
DT = 0.002 # Example: 2 fs time step DT = 0.002 # Example: 2 fs time step
PDB_FOLDER_PATH = Path("./pdb_test") # Assuming the PDB files are in a folder named 'pdb_files' in the current directory PDB_FOLDER_PATH = Path("./pdb_gjm") # Assuming the PDB files are in a folder named 'pdb_files' in the current directory
# 传入自定义的bash脚本路径 # 传入自定义的bash脚本路径
CUSTOM_BASH_SCRIPT_PATH = Path('md_gromacs.sh') CUSTOM_BASH_SCRIPT_PATH = Path('md_gromacs.sh')
# 传入 GMXRC 文件的路径 # 传入 GMXRC 文件的路径