Running Lattice Minimization

[Yu-Tang-Lin]

In the example folders, I tried to running lattice minimization

1. I followed README to run this run_xtal_md xml -i build_system/oxamide/1473522_gaff1.xml -p xtal_min/oxamide_gaff1/1473522_gaff1_min.pdb --temperature=298.15 --nanoseconds 2 --prefix xtal_md/oxamide_gaff1 but got FileNotFoundError.
2. I run this run_xtal_md xml -i build_system/oxamide/1473522_gaff1.xml -p xtal_min/oxamide_gaff1_min.pdb --temperature=298.15 --nanoseconds 2 --prefix xtal_md/oxamide_gaff1 instead, in order to link the correct input (I think) .
3. Still got an FileNotFoundError but a different FileNotFoundError.
   FileNotFoundError: [Errno 2] No such file or directory: './/run_0/xtal_md/oxamide_gaff1_thermalization.xml' Not sure what is run_0 or oxamide_gaff1_thermalization.xml, but I did not see any files in my run_0 folder.

[wutobias]

Thanks @Yu-Tang-Lin. I have fixed this and several other issues with the examples. Could you please have a look and try again? Thanks!