Bespoke Torsional Fitting with FFPOPT

Learning Objectives

Use FFPOPT to Run Dihedral Scans for a Simple Molecule
Use FFPOPT with a Machine Learning Potential to Fit New Dihedral Parameters

[4]:

print(1 + 2)

Note: This is an important note for the reader.

Linear Dihedral Scans

The first type of scan we will do, with a standard force field, is a traditional linear torsional scan. This is done by specifying a range of angles to scan over and the number of points to sample. These types of scans usually start at the natural dihedral angle (the angle that the dihedral takes after an unconstrained minimization), and then scans are done in both the positive and negative directions to span 360 degrees.

In the FFPOPT package, these normal types of dihedral scans are called using the ffpopt-DihedScan.py script. This script takes a number of command line arguments, which are described in the help message. You can see the help message by running the following command:

[8]:

python3 ffpopt-DihedScan.py -h

  Cell In[8], line 1
    python3 ffpopt-DihedScan.py -h
            ^
SyntaxError: invalid syntax

The main arguments you will need to specify are: