REMINDER : up-to-date python not tested, please use python3.8 for stability

[quantaosun]

Directly installing the packages from the ipynb file may not work, because many packages have not been updated to the newer python environment. You can work it out yourself but it would take some time to do so, Please use the environment.yml file (which has fixed the python to 3.8.16 for example, but if using colab, the python is up-to-date version maybe 3.11 in April 2024 and cause incompatible issues with other packages) when possible, and it should still work until April 2024.

Also, it is a bit slow even with v100 colab provided to run the simulation, please consider use RTX4090 is recommended when availiable.

[yanbosmu]

When I run Dock-MD-FEP-local_installation.ipynb, there is an error.

NameError Traceback (most recent call last)
Input In [11], in <cell line: 159>()
156 for line in f:
157 vol = float(line.split()[1])

NameError: name 'vol' is not defined--> 159 vol_lit = vol * pow(10, -27)
160 atom_lit = 9.03 * pow(10, 22)
161 conc = float(Concentration)

NameError: name 'vol' is not defined

!grep "Volume:" leap.log > temp.txt
with open("temp.txt", 'r') as f:
for line in f:
vol = float(line.split()[1])

There is no Volume in leap.log，so it is empty in temp.txt.
Any solution to this?
thank you