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emerbitz merged 1 commit into from
Dec 19, 2025
Merged

add lj params example #3

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23 changes: 22 additions & 1 deletion examples/ff_params/ff_params.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,8 @@
original_top = Topology(top_dict)

# %% [markdown]
# # 1. Manipulation of partial charges
# # 1. Manipulation of nonbonded parameters
# ## 1.1 Manipulation of partial charges
# Example: Change the charge of the CB atom of the first Ala residue and its attached H atoms
# %% [markdown]
# Inital charges
Expand Down Expand Up @@ -69,6 +70,26 @@
out_path = Path("hexala_mod_charges.top")
top.to_path(out_path)
# %% [markdown]
# ## 1.2. Manipulation of Lennard-Jones parameters
# Example: Change the Lennard-Jones parameters of the CT atom type.
# %% [markdown]
# Inital LJ parameters:
# %%
top = deepcopy(original_top)
print(top.ff.atomtypes["CT"])
# %% [markdown]
# Modify LJ parameters:
# %%
top.ff.atomtypes["CT"].sigma = "0.35" # New sigma value in nm
top.ff.atomtypes["CT"].epsilon = "0.8" # New epsilon value in kJ mol-1

print(top.ff.atomtypes["CT"])
# %% [markdown]
# Now, let's write the modified topology to a new file, called "hexala_mod_lj.top".
# %%
out_path = Path("hexala_mod_lj.top")
top.to_path(out_path)
# %% [markdown]
# # 2. Manipulation of bonded parameters
# ## 2.1. Local parameter modification
# Simillar to the partial charges, the force field parameters can be modified of a single bond angle or dihedral. <br>
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