FFPOPT Quick Start Guide - Installation
=======================================

| Zeke A. Piskulich\ :sup:`1`,  and Darrin M.
  York\ :sup:`1`
| :sup:`1`\ Laboratory for Biomolecular Simulation Research, Institute
  for Quantitative Biomedicine and Department of Chemistry and Chemical
  Biology, Rutgers University, Piscataway, NJ 08854, USA

Learning objectives
-------------------

.. start-learning-objectives

-  Learn how to install the FFPOPT package and its dependencies

.. end-learning-objectives

Relevant literature
-------------------

- Coming Soon!


Tutorial
--------

.. contents::
   :local:
   :depth: 4

.. start-tutorial


In this tutorial, we will be using a small molecular fragment that contains a deprotonated amide. These fragments can show up in certain ligands, and are presently a challenge for standard force field generation within amber. We will walk through how to use FFPOPT to scan dihedral angles with both MD force-fields and machine learning potentials, and then we will walk through the process of fitting new dihedral parameters.

Installation
~~~~~~~~~~~~

To run this tutorial, you will need to have `FFPOPT` installed. You can find the installation instructions in the `FFPOPT` GitHub repository: `FFPOPT GitHub <https://github.com/tjgiese/ffpopt>`.

Installation instructions may be found in the readme file. You will also need to have `AMBER` installed, as well as `Python 3.7+` with the `numpy` and `scipy` libraries.

.. important::

   **Amarel Users** - Good News! `FFPOPT` is already installed on Amarel. You can load it using the following command:

    .. code-block:: bash
  
        module purge
        module use /projectsp/f_lbsr/YorkGroup/software/23jun25/modulefiles
        # One of these two lines, depending on the ML potential you want to use
        #module load 23jun25/ffpopt/21aug25.g-pytorch
        #module load 23jun25/ffpopt/21aug25.g-psi4

.. note::

  If you are using actual PSI4 for quantum calculations, this introduces incompatibilities with other packages. It is recommended to use the `psi4` version of `FFPOPT` for this tutorial. These instructions are included in the ReadMe.

If you are running this tutorial on your local machine, you can install `FFPOPT` and its dependencies using the following commands:

.. code-block:: bash

  # Local Installation example
  git clone https://github.com/tjgiese/ffpopt.git
  cd ffpopt
  wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
  bash ./Miniforge3-Linux-x86_64.sh -b -f -p ${PWD}/miniforge3
  source ${PWD}/miniforge3/bin/activate
  conda install -y dpdata deepmd-kit ase parmed dacase::ambertools-dac=25 dftd3-python rdkit
  python3 -m pip install torch torchvision torchaudio
  python3 -m pip install cmake tblite mace-torch geometric aimnet torchani
  conda deactivate
  source ${PWD}/miniforge3/bin/activate
  cd build
  bash ./run_cmake.sh


.. end-tutorial