Hello everyone, Sanket here. Welcome to another video, another tutorial on my channel. Today we are going to discuss and look into what exactly is molecular dynamics simulations. We will be performing a tutorial for molecular dynamics simulations using a software which is called Gromacs. So, molecular dynamics

simulations were first carried out in 1977 by McCammon. He performed the simulation on BPTI, also called bovine pancreatic trypsin inhibitor. The paper was published in Nature on the 16th of June 1977, and the PDB

structure for it was later available after a few years in the Protein Data Bank. The PDB ID for the structure, that is the bovine structure, is 2CGT. So you can go and check it. So what exactly is molecular dynamics simulations? So molecular dynamics simulations is a

simulation which helps us to analyze the movement of atoms or molecules. So each and every biomolecule has molecules and they have atoms. When we are talking about MD simulation of a biological protein, this biological protein is there in our cells, okay? And you know that all our cells have about

80 to 90 percent water. Okay? So how do these biomolecules react or behave when they are kept in any particular solution? So it can be a water solution or it can be some other liquid solution, or how does a biomolecule react when it passes through a

bilayer membrane? So this is what all you can analyze by performing simulations. This is what we call as your molecular dynamics simulations. The atoms and the molecules which are there, okay, they interact for a fixed period of time. So this fixed period of time can

be for particular nanoseconds, or it can be for a particular sentence. This evolution, what we see, is called dynamic emulation. So when I'm saying movement, I mean to say how these atoms or these molecules move when they interact with different liquids.

molecules, as you see, yeah. Or if it's the abaya lipid bilayer molecules as they pass through the cell membrane. So all of this, I mean, experimentally you can analyze, you know, by looking at the peaks or looking at the graphs, or

looking at the color change, you can do that. But when you want to see something, actually, how a protein is behaving, okay, that is where your bioinformatics comes into play. So you can say, OMG, simulation sort of shows a small, short movie of how a protein behaves in a biomolecule

solution. So your molecular dynamics, it follows Newton's equation, okay, and specifically it follows the second law of Newton's equation, where your force exerted is based on the mass and the acceleration. What is that? So that means that if your mass is greater,

the force which is applied to it will be greater. If your force is less—sorry, if the mass is less—the force applied to it will be less. This is the same concept, the same fundamental principle, when you're performing MD simulations for any

So if your molecular mass of the protein, or the protein of any—or any other biomolecule, for that matter—can be DNA or anything. So if your biomolecular mass is great, then the force which is applied to the atoms and the

Molecules to move will be great if the molecular weight is small; then the force which is applied will be so small. Okay, so yeah, so your MD simulations, what they do is they follow Newton's second law: F=ma. Now what

are the steps of these molecular dynamics? Alright, there are three crucial steps. Okay, there is creation of the initial step, introduction of interaction potentials, and third is to predict how a particle will move. So this particle can be any of your biomolecules, as I stated earlier, so

the first one, that is, creation of the initial step; there are three sub-steps: one is to generate a topology file for the protein; second is to add a box and add solvation to the system. Okay, add boxes—you add a box around your protein. Solvation means you add water

molecules to the system, again, or any liquid to the system. Third, in your initial step, is you add ions. So sometimes, you know, you have biomolecules which do not have a particular charge to them, so there are some ions which are less. So in this case,

you can add ions in order to bring equilibrium to the system. So these are the three steps in your initial step. Then the fourth is introduction of interaction potentials, where you carry out—the fourth step is where you carry out your energy minimization step. Okay, energy minimization is nothing but where

you bring down the overall energy of the biomolecule in order to make it much more stable. This energy minimization step—you can see if you're, when you're performing docking, what exactly is docking—you can go to my other video on molecular

Docking using AutoDock Vina, where you can understand how the energy minimization step is done. But, in homology modeling, important work is to carry out energy minimization in docking.  In eukaryote MD simulations, you carry out energy minimization.

Minimization and the last two steps are equilibration of the system and your final MD production run. Okay, so your equilibration of this system is nothing but equilibration with constant pressure, constant temperature, and constant volume. So I repeat again: three important

things: constant pressure, constant temperature, and constant volume. Keeping these three things constant, we run the simulation for your biomolecule. What is there? So in this tutorial for molecular dynamics simulations, we will be performing all of these six steps. So I think when we perform all six steps,

you will be able to understand it much better. We will be performing MD simulations using software called Gromacs. This Gromacs is software which is freely available. So this is the tutorial. You can go to Google and type 'Gromacs tutorials'. Then you can go to MDtutorials.com.

You can click on the first one, that is lysozyme in water, and then you can click 'Start tutorial'. So we will be going through each and every step. Each of the steps for the Gromacs tutorial are given here, like the one

which I showed you in the PPT slides also. So we'll be going through all of them. For the commands to be followed in Gromacs, you can refer to this tutorial and copy the commands which are there. Okay, so for performing a Gromacs tutorial, we would require a Linux

Operating system. So I think let's start with the tutorial. Yeah, so this is your home page for our CSB. The first thing we're going to do for lysosome in water is we're going to download the structure for lysosome from PDB.

So the PDB ID for lysosome is 1AKI. So you go to PDB, type 1AKI, and then we download the PDB protein. So it will be saved as 1aki.pdb in your downloads. Yeah. So we take this PDB ID and then we

create a folder, probably you can create a folder called 'lysosome in water', and then we can save that 1aki.pdb in your folder. Now the next thing is we actually start performing your Gromacs. How to do it? First, go into the

folder where we're going to perform it. So it's—we had it—it was in Documents and was in 'lysosome in water'. So once I'm there, here I will start the command. So the first command is `gmx -h OH` then the name of the PDB, that is

1aki.pdb, then `>` space `1aki_clean.pdb`. Now what this is going to do is it's going to clean the extra water molecules or HOH—water molecules which are there. So as you can see, it's a protein

preparation step that has been carried out right now. Okay? And you can see that 1aki_clean.pdb has been created. So the first thing, where your protein preparation step has been performed, okay? Now let's move to the next step. Okay, the next step is what we

We're talking about your well protein, so now we are going to process the protein. So how do you actually process the protein? So it's minus F here, so we do gmx then we go -f. That was your file here. Okay, -f file is your 1AKI_

underscore clean. But PDB file - oh, that is your output. It will be 1AKI_processed. So this is the first step. If you remember the steps, okay, it's the first step is your protein processing step. So it is what 1AKI_processed.

gmx pdb2gmx. Okay, it's pdb2gmx. All right, so what we have here are the 15 force fields. Okay, you can see Amber, CHARMM, Gromos,

OPLS. Here we'll go for OPLS. Okay, so we'll type 15 and then click Enter. Yeah. So what has happened? Yeah, if you can see, you can see your 1AKI_processed. Oh, you can see your topol.top. Topol.top is your topology file which

has been created and your pos1.itp file. It is your pos1.itp file which has been created. What I will do is I will again show you how to... I'll open this topol.top file for you. Yeah, so this is how a topology file looks like. This

my dear friends, is the most important file. Okay, we will be requiring this file and needing to open this file as embedded. So you can see protein_chain, in which is there, and these are the various amino acids and their atoms as well as coordinates and the charges which is there. So try and

Understand this is one of the most important files now. HPC, by the way – water.hpc was one of the water molecule okay, which we had applied. Now we'll go for the next one, which is… the next step is `gmx editconf -f -o EK`

underscore process. So `-f` is the file input, so that is your `process.gro` file. What has been done? `.gro` because it said `romax -o 1ake I wanna ki_newbox`. So now we are going to go for creation of the box. If you remember the

second step was, we are creating the box. So it is `-c -d 1.0`. So that is the dimension, okay? The dimension is 1.0 and let us make it as a cubic shape, so that's what `-bc cubic`. And if

you click on Enter, yeah. Now we have created the volume. If you can see the various vectors, the angles, how… that is the shape of the molecule box. The dimensions of the box, we can see what is the volume, what is the system size, etc.

What is the diameter, okay? And the box which is going to be created is in the cubic format. The next step is to add solvation, okay? Now the box is created. Next step is to add solvation. So `gmx solvate`. Now here in this step we are

adding the water molecules. So `-cp 1ake newbox`. So inside this new box, the cubic newbox, we are going to add water. So `-cs spc -16`. So this is one type of water molecule what we are adding. So k

So, this is by default what you see: grow files which are present inside your GROMACS directory. When you're installing GROMACS, all of this is initially there, and the output will be 1aki_solv.gro. So we are now creating a solvation file with the protein inside, and the product of this is very important. You have to add the topology file. So now our topology file, that top or .top file, is updated and the solvation step has taken place. So now we will be having a .gro file if you can

see. Yeah, the first thing is your topol.top; this is the topology file which is there. If I go down, yes, can you see? There is solv.gro.  10,644 water molecules are added, okay, and your protein

chain is one, which is there. Okay, so we have created the new box; we have added the 10,644 solvation molecules. Now what I would like to show you is how it actually looks, okay? So how does it look like? Yeah, so what I do is I open it. Yeah, okay.

I open this solv.gro. Can you see this? Okay, in VMD I'm opening the solv.gro. Can you see the cube-shaped box? The red ones are your water molecules, and the one which is in the blue, bottom inside, is your protein. So this is how a solvation

step actually looks like. So we are finished right now by generating the topology file, that was your 1aki.top, and this could persist or .gro. We are finished doing both: creating a box, which was 1aki_newbox.gro. All right, so a new box was actually created.

And the shape of the box was a cubic, okay? And the solvation step, which was one, Aki underscore Soloff dot gro. Okay, so that solvation added the water molecule. So if there was an SPC.e.gro, it is, as I told you, by default,

when you install Gromacs, many, not many, you can see backend files are created. So one of them, a solvation file. So we created the topology file, the box file will be created, and the solution file. Now, the next step is what we'll be creating is your ions.

So in the next video, we'll be performing how to add ions to your system. Hopefully, you have understood how to create a topology and box file. All right, so thank you.

Molecular Dynamics Tutorial | Lysozyme in Water: GROMACS - PART 1

Molecular Dynamics Tutorial | Lysozyme in Water: GROMACS - PART 1

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