Preparing a protein to run an atomistic Molecular Dynamics simulation
========================================================================

Overview
---------

This **use case** aims to illustrate the process of setting up an **atomistic
Molecular Dynamics simulation** system containing a **protein**, step by step.
The particular example used is the **Parvalbumin Calcium-binding** protein
(PDB code `1B8R <https://www.rcsb.org/structure/1B8R>`_).

**Parvalbumin** is a calcium binding protein that is found in subsets of sensory
**neurons**, inhibitory **interneurons** and **motoneurons**. Alterations in the
function of parvalbumin-expressing **neurons** have been implicated in various
areas of clinical interest such as **Alzheimer's disease**, **autism**,
**schizophrenia**, age-related **cognitive defects** and some forms of **cancer**.

Background
-----------
**Molecular Dynamics (MD) simulation** is the most popular theoretical technique to
obtain **macromolecular dynamic information**. **Classical mechanics** is used to represent
**atoms as spheres** of a given radius, hardness, charge and mass. The **energy functional** used by
**force-fields** is usually composed of two terms: **bonded** and **non-bonded** components:

.. math::
	E_{pot} = E_{bonded} + E_{non-bonded}

where

.. math::
  E_{bonded} = E_{bond} + E_{angle} + E_{dihedral}

and

.. math::
  E_{non-bonded} = E_{elec} + E_{VdW}


.. figure:: MD.png
 :width: 500pt

The combination of the **force-fields** with the **laws of classical mechanics**
(Newton’s second law of motion), allows the calculation of the
**time evolution** of the system.
**Trajectories** of atoms and molecules are determined by numerically solving
Newton's equations of motion for a system of interacting particles, where forces
between the particles and their potential energies are calculated using
the **force-field energy functionals**.

How it works ?
--------------

This workflow makes extensive use of the **BioExcel Building Blocks library**
(`biobb <https://github.com/bioexcel/biobb>`_). Each step of the process is
performed by a **building block** (bb), which are wrappers of tools/scripts
that computes a particular functionality (e.g. Solvating a system).
If you are interested in expanding/modifying the current workflow,
please visit the **existing documentation** for each of the packages
`here <https://github.com/bioexcel/biobb>`_.

Most of the steps performed in this pipeline run **GROMACS MD package** tools,
one of the most popular MD packages available.

Although the **pipeline** is presented **step by step** with associated
information, it is extremely advisable to previously spend some time reading
documentation about **Molecular Dynamics simulations**, to get familiar with
the terms used, especially for newcomers to the field.
This workflow is based on the official **GROMACS MD setup tutorial**:
http://www.mdtutorials.com/gmx/lysozyme/index.html

Outcomes / Steps
----------------

This use case will explain:

•	How to fetch a **PDB structure** from the **RCSB PDB database**
•	How to **fix a protein structure** (add missing atoms)
•	How to create a **protein system topology**
•	How to create a **solvent box** surrounding the protein
•	How to fill the box with **water molecules**
•	How to **energetically neutralize** the system with the addition of **counterions**
•	How to **energetically minimize** the system
•	How to **equilibrate** the system in two steps (NVT, NPT)
•	How to run a **free Molecular Dynamics (MD) simulation**
•	How to **post-process** and **visualize** the resulting **3D trajectory**
•	How to **find** and **download** the generated **output files**

Input
------
- A **PDB code** of a **protein structure**

Outputs
-------
- **Interactive and 3D vizualisation** of the **intermediate results** on the protein structure
- **Interactive and 3D vizualisation** of the **resulting trajectory**
- **Interactive visualization** of **2D analyses plots** (energies, temperature, RMSd)
- Short (100ps) **trajectory file** generated from the final **free MD simulation** step
- Collection of **files needed to extend the MD simulation** available to download

Targeted audience
-----------------
All scientists working in biology related areas where protein study is relevant
with a focus on **structural biologists** and **biochemists**. Especially directed to
scientists interested in **protein dynamics** and **flexibility**.