Tutorial । Protein-Protein Complex Simulation ।। GROMACS ।। SIM Protein

This tutorial will guide a new user through the process of setting up a simulation system containing a protein complex in a box of water, with ions.
Each step will contain an explanation of input and output, using typical settings for general use.

GROningen MAchine for Chemical Simulations (GROMACS) is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. It was
originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers
worldwide. GROMACS is one of the fastest and most popular software packages available, and can run on central processing units (CPUs) and graphics processing
units (GPUs). It is free, open-source software released under the GNU General Public License (GPL), and starting with version 4.6, the GNU Lesser General Public
License (LGPL).

DISCLAIMER
In this video tutorial, 4mn8.pdb have been used for demonstration. The parameters in this tutorial are used not universal or applicable for all protein structure file.
Different protein structure files need different parameters (box size, ions, trjconv etc.). Before simulating any protein structure file, read through the corresponding paper
to understand the structure. Though the basic and sequences of protein structure simulation by using GROMACS are same as shown in this video.

In this video tutorial just procedures have been demonstrated. Protein-Protein complex simulation is a lengthy process. If you follow these steps properly without facing any
errors, you will get final simulated file for analysis.

Protein-Protein Complex Simulation Tutorial: sites.google.com/g.bracu.ac.bd/sbio/simulation/…
RCSB: rcsb.org/

Background Score: youtube.com/watch?v=RZu-gReMNRo


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