Gromacs/C3/Visualization-With-VMD/English - Revision history

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Ranipv076: Created page with "{| border=1 | | '''Visual Cue''' | | '''Narration''' |- | | '''Slide Number 1''' '''Title Slide ''' | | Welcome to the tutorial '''Visualization With VMD''' of '''Gromac..."

2022-02-01T08:56:55Z

Created page with "{| border=1 | | '''Visual Cue''' | | '''Narration''' |- | | '''Slide Number 1''' '''Title Slide ''' | | Welcome to the tutorial '''Visualization With VMD''' of '''Gromac..."

New page

{| border=1
| | '''Visual Cue'''
| | '''Narration'''

|-
| | '''Slide Number 1'''

'''Title Slide '''
| | Welcome to the tutorial '''Visualization With VMD''' of '''Gromacs''' generated files.

|-
| | '''Slide Number 2'''

'''Learning Objectives'''
| | In this tutorial, we will learn to,

* Open a '''Gromacs''' generated trajectory file
* Play and view the frames in the trajectory
* Color and display structures from selected frames

|-
| | '''Slide Number 3'''

'''Learning Objectives'''
| |
* Create a movie from the trajectory
* Align structures from two different states of the protein

|-
| | '''Slide Number 4'''

'''System and Software Requirement'''
| | To record this tutorial, I am using

* '''Ubuntu Linux''' v20.04 OS
* '''VMD''' 1.9.3
* '''VLC''' media player 3.0.8

|-
| | '''Slide Number 5'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
| | To follow this tutorial, * Learner must be familiar with basics of '''VMD'''.
* For pre-requisite tutorials, please visit this site.

|-
| | '''Slide Number 6'''

'''Code Files'''
| |
* Files used in this tutorial are provided in the code files link.
* Please download and extract the files.
* Make a copy and then use them while practising.

|-
| | Copy the provided folder with input files to the '''Desktop''' directory.
| | Copy the provided folder containing the input files to the working directory.

'''VMD''' can open the '''trr, gro''' and '''pdb''' files present here.

|-
| | Show input files in the file manager.
| | The '''npt.trr''' is a trajectory file, which is readable by '''VMD'''.

This file was generated in the pressure equilibration step.

It contains the many conformational states of the protein during the simulation.

|-
| |
| | Let’s open the '''npt.gro''' file in '''VMD'''.

|-
| | Open a '''terminal'''.

Type '''VMD npt.gro''' at the terminal prompt.

Press '''Enter'''.
| | Open a '''terminal''' and change path to the working directory.

The '''gro''' file is the final output of the '''npt''' step from '''Gromacs'''.

|-
| | The molecule '''npt.gro''' gets loaded.
| | This is the starting structure file for the '''MD''' simulation of the protein.

Text annotation: Windows users must open '''VMD''' first, then open the '''gro''' file through '''VMD'''.

|-
| | Click on '''Graphics, Representations'''.
| | Let’s change the display mode and show only the '''protein''' for clarity.

|-
| | In the '''Selected atoms''' form, type '''protein''' and press '''Enter'''.
| | In the '''Selected Atoms''' form enter '''protein'''.

Now water molecules get hidden.

|-
| | For '''Drawing method''', choose '''Ribbons'''.
| | For '''Drawing method''', choose '''Ribbons'''.

|-
| | In the '''VMD''' terminal enter the command '''pbc box'''.
| | I will also display the box with the '''pbc space box''' command.

|-
| | Show '''VMD''' graphics window.
| | Let’s ascertain the protein is not split into parts in the box.

It may happen so and due to the '''periodic boundary condition'''.

|-
| |
| | If such a situation is observed, user must rerun the equilibration step.

|-
| | Click on '''File, New Molecule'''.
| | Let’s next load the trajectory file.

Click on '''File, New Molecule'''.

|-
| | In the '''Load Files for''' pulldown, choose the '''npt.gro''' molecule.
| | In the '''Load Files for''' pulldown, choose the '''npt.gro''' molecule.

|-
| | Click on '''Browse''', choose '''npt.trr'''.

Click on '''Ok''' and then on '''Load'''.
| | Click on '''Browse''', choose '''npt.trr'''.

Click on '''Ok''' and then on '''Load'''.

|-
| | Close the '''Load''' window.
| | Let’s close the '''Load''' window.

The trajectory file is loaded to a structure by '''VMD'''.

|-
| | Show loading of all the states.

Show number of frames in the '''Main window'''.
| | '''VMD''' loads all the conformational states of the protein from the '''trajectory''' file.

These are called the different frames.

The number of frames or states, in the '''trajectory''' is also displayed here.

|-
| | Click on the play button.
| | Next, click on the play button, seen on the lower right end of the main window.

|-
| | Show the playing of the trajectory.
| | Notice, all the states in the trajectory being played.

|-
| | Play the trajectory.
| | The duration of the '''equilibration''' step is short.

|-
| | Slide the speed slider to slow it down.
| | We can also adjust the speed at which the states are played.

|-
| | Click on pause and step buttons.
| | We can pause and step through the states of the trajectory as seen here.

|-
| | Click on '''Graphics, Representations'''.
| | Now, let’s view the chloride ions, which are present in the system .

For this, first click on '''Graphics, Representations'''.

|-
| | Click on '''Create New rep'''.
| | Then, click on '''Create New rep'''.

|-
| | In the '''Selected atoms''' form, type '''name CL''' and press '''Enter'''.
| | In the '''Selected Atoms''' form enter '''name CL'''.

|-
| | For '''Drawing method''', choose '''beads'''.

Close the '''Representations''' window.
| | For '''Drawing methods''', choose '''beads'''.

Close the '''Representations''' window.

Notice the 8 chloride ions.

|-
| | Play the trajectory again.
| | Now, play the '''trajectory''' file again.

|-
| |
| | Notice that, the '''chloride''' ions, being smaller, moves faster than the protein.

This movement is due to diffusion.

|-
| | Show the ion exiting the box and being added back.
| | Occasionally, an ion exits the box and it gets added back to the box.

This is due to the '''periodic boundary condition''' which was set up in the '''mdp''' file.

|-
| |
| | Let’s make a movie of all the frames in the trajectory.

|-
| | Click on '''Extensions, Visualization''' and choose '''Movie Maker'''.
| | For this click on '''Extensions, Visualization''' and choose '''Movie Maker'''.

|-
| | The '''VMD Movie Generator''' window opens.
| | The '''VMD Movie Generator''' window opens.

|-
| | Click on '''Set working directory'''.

In the dialog box, change to '''Videos''' folder.
| | I will first '''Set the working directory'''. Click on it.

In the dialog box, change to the '''Videos''' path to save the videos.

You may choose this directory as you desire.

|-
| | Click on '''Movie settings''' and choose '''Trajectory'''.
| | Click on '''Movie settings''' and choose '''Trajectory'''.

|-
| | Click on '''Format''' and choose '''MPEG-2 (ffmpeg)'''.
| | Click on '''Format''' and choose '''MPEG-2''' '''(ffmpeg)''' to choose the video format.

|-
| | Click on '''Renderer''' and hover over '''Snapshot'''.
| | For '''Renderer''' I will retain '''Snapshot'''.

This captures each frame as seen in the graphics window.

|-
| | In '''Name of movie''' field, type '''firstmovie'''.
| | For '''Name of movie''', I will enter '''firstmovie'''.

|-
| | Hover over '''trajectory''' step and duration.
| | Now, the '''trajectory''' step is 1 and movie duration is 4 seconds now.

I will retain the defaults.

|-
| | Click on '''Make Movie'''.
| | Click on '''Make Movie''' and notice the progress.

|-
| | Close the '''VMD Movie Generator''' window.
| | After the process is completed, close the '''VMD Movie Generator''' window.

|-
| | Open file manager and go to the '''Videos''' folder.
| | Open the file manager and go to the '''Videos''' folder where the movie was created.

|-
| | Open the '''firstmovie.mpg''' file.
| | Open the '''firstmovie.mpg''' file.

I will use '''VLC''' media player for it.

|-
| | Play the '''firstvideo.mpg''' video.
| | Pause the tutorial video and play the movie that you just created.

|-
| | Close '''VLC''' and go back to '''VMD'''.
| | I will close '''VLC''' and let’s go back to '''VMD'''.

|-
| | Open the graphical representations window.
| | Next, let’s display color and select frames for display from the trajectory.

Go to the graphical representations window.

|-
| | Show '''Selected atoms''' form with '''npt.gro''' molecule selected.
| | Make sure that the '''npt.gro''' molecule is selected as seen.

|-
| | In the Coloring methods pulldown, select '''Trajectory''' and choose'''Timestep'''.
| | In the '''Coloring method''' pulldown, select '''Trajectory''' and choose
'''Timestep'''.

|-
| | Cursor on '''Drawing method'''.

Click on the play button in '''VMD''' main window.
| | You may change the '''Drawing method''' if desired.

Now, play the '''trajectory'''.

|-
| | Show color change in the graphics window.
| | Notice the starting frame is red by default and ending frame is in blue color.

|-
| | Click on play again to stop.
| | I will stop to play the frames.

|-
| | Go to '''Representations''', and select the '''Trajectory''' tab.
| | Go to '''Representations''', and select the '''Trajectory''' tab.

|-
| | Cursor on '''Draw multiple frames'''.
| | By default, '''Draw multiple frames''' is set to '''now''', which is the current frame.

|-
| | Type, '''0:20:102''' in the '''Draw multiple frames''' form.
| | To show every 20 frames, type 0 colon 20 colon 102.

My '''trajectory''' range is 0 to 102 and hence the limits are specified.

|-
| | Show the 5 displayed frames.
| | Now, notice the 5 frames that are displayed in the graphical window.

|-
| |
| | Next, let’s choose specific user selected frames for display.

|-
| | In the '''Draw multiple frames''' form, Type, '''1 and 49 and 100''' and press '''Enter'''.
| | Say I want to display, 1st, 49th and 100 th frame only.

In the form, type, '''1 and 49 and 100''' and press '''Enter''' as seen.

|-
| | Show the displayed frames in graphical window.
| | This will show the three specified frames.

|-
| |
| | Let’s compare the '''npt.gro''' structure with the starting structure of '''first.gro'''.

We will read both molecules and align them for comparison.

|-
| | In the '''Draw multiple frames''' form, Type, '''now''' and press '''Enter'''.
| | First I will reset the display to the present frame.

Then alignment process will be clearly visible.

|-
| | Click on '''File, New Molecule'''.

Click on '''Browse''', choose '''first.gro'''.

Click on '''Ok''' and then on '''Load'''.

Close the Window.
| | Close the representations Windows.

Let’s read in '''first.gro'''.

'''First.gro''' has hydrogens added to it.

It’s precursor, '''1aki.pdb'''.

Both molecules have the same number of atoms in the protein.

|-
| | Click on '''Graphics, Representations'''.
| | Click on '''Graphics, Representations'''.

|-
| | Choose the '''protein representation'''.
| | Choose the '''protein representation'''.

|-
| | For '''Drawing method''', choose '''Lines'''.
| | For '''Drawing method''', choose '''Lines'''.

Let’s show all the atoms and bonds of the protein from '''npt.gro''' file also.

|-
| | Rotate the graphics window to show both the molecules.
| | The loaded structures may not be discernible separately.

If so, rotate them in the graphics window to view them.

|-
| | Cursor on the graphics windows.
| | Now the two molecules are not aligned with each other.

Hence possible conformational differences are not seen clearly.

Let’s align the two molecules or overlay them .

|-
| | Click on '''Extensions''' and '''Tk console'''.
| | For this first click on '''Extensions''' and '''Tk console'''.

A '''VMD TKconsole''' window opens.

|-
| | Type, '''set sel0 [atomselect 0 protein] '''and press '''Enter'''.
| | Type the command as seen and press '''Enter'''.

This selects all atoms in the protein from the first structure.

|-
| | Type, '''set sel1 [atomselect 1 protein] '''and press '''Enter'''.
| | Now select all the atoms from the second structure using the command as seen.

|-
| | Type, '''set A [measure fit $sel0 $sel1]''' and press '''Enter'''.
| | This command '''fits''' the positions of the atoms in the two protein molecules.

The '''fit''' command works, only when the number of atoms are the same.

|-
| | Type, '''$sel0 move $A''' and press '''Enter'''.
| | The move command, '''realigns''' the position of the molecule in the graphics window.

The coordinates of the first molecule is aligned with that of the second.

|-
| | Cursor in '''VMD''' graphics window.
| | The change in positions and conformational change if any is clearly seen.

|-
| | '''Slide Number 7'''

'''Summary '''
| | Now let’s summarize. In this tutorial, we,

* Loaded a trajectory file
* Played and viewed frames from the '''trajectory'''
* Created a movie using the frames in the '''trajectory'''

|-
| | '''Slide Number 8'''

'''Summary'''
| |
* Changed color and viewed selected frames
* Aligned the starting and equilibrated structures of the protein

|-
| | '''Slide Number 9'''

'''Assignment'''
| | For assignment activity, please do the following.

Answer the following question.* Can '''1AKI.pdb''' be aligned with '''npt.gro''', with the '''measure fit''' command?
* Explain the reasoning and demonstrate it

|-
| | '''Slide Number 10'''

'''Assignment'''
| | * Create a new representation for '''npt.gro''' molecule
* In '''Selected atoms''' enter, '''''water and within 2 of protein'''''
* This displays water molecules present only within 2A of protein

|-
| | '''Slide Number 11'''

'''Assignment'''
| | * Play the trajectory and notice the movement of water molecules

|-
| | '''Slide Number 12'''

'''Spoken Tutorial Project'''
| | This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
| | '''Slide Number 13'''

'''Spoken Tutorial workshops'''
| | We conduct workshops using spoken tutorials and give certificates.

Please write to us.

|-
| | '''Slide Number 14'''

'''Forum for questions'''
| | Post your timed queries in this forum.

|-
| | '''Slide Number 15'''

'''Acknowledgment'''
| | Spoken Tutorial Project is funded by MoE, Government of India.

|-
| |
| | This is Rani from IIT, Bombay. Thank you for joining.

|-
|}

@@ Line 363: / Line 363: @@
 Then alignment process will be clearly visible.
 |-
@@ Line 372: / Line 376: @@
 | | Let’s read in '''first.gro'''.
 '''First.gro''' has hydrogens added to it.
@@ Line 381: / Line 382: @@
 Both molecules have the same number of atoms in the protein.
 |-
@@ Line 395: / Line 397: @@
 Let’s show all the atoms and bonds of the protein from '''npt.gro''' file also.
 |-

@@ Line 475: / Line 475: @@
 '''Assignment'''
 |  | * Create a new representation for '''npt.gro''' molecule
-* In '''Selected atoms''' enter, '''''water and within 2A of protein'''''
+* In '''Selected atoms''' enter, '''''water and within 2 of protein'''''
 * This displays water molecules present only within 2 angstroms of protein

@@ Line 84: / Line 84: @@
 Press '''Enter'''.
-|  | Open a '''terminal''' and change path to the working directory.
+|  | The '''gro''' file is the final output of the '''npt''' step from '''Gromacs'''.
-−
 The '''gro''' file is the final output of the '''npt''' step from '''Gromacs'''.
 |-

@@ Line 370: / Line 370: @@
 Click on '''Ok''' and then on '''Load'''.
-| |
+| | Let’s read in '''first.gro'''.
 |-
-| |Close the Window.
+|  |Close the Window.
 |  | Close the representations Windows.
 '''First.gro''' has hydrogens added to it.
-It’s precursor, '''1aki.pdb'''.
+It’s precursor is, '''1aki.pdb'''.
 Both molecules have the same number of atoms in the protein.
@@ Line 400: / Line 398: @@
 |-
 |  | Rotate the graphics window to show both the molecules.
-|  | The loaded structures may not be discernible separately.
+|  | Then, the loaded structures may not be discernible separately.
 If so, rotate them in the graphics window to view them.
@@ Line 406: / Line 404: @@
 |-
 |  | Cursor on the graphics windows.
-|  | Now the two molecules are not aligned with each other.
+|  | Now the molecules are not aligned properly, to view any conformational differences.
-−
-−
-Hence possible conformational differences are not seen clearly.
-Let’s align the two molecules or overlay them .
+Hence, we will align the two molecules or overlay them .
 |-

@@ Line 75: / Line 75: @@
 |-
-|  | Open a '''terminal'''.
+||Showm opening a '''terminal''', changing to working directory and
-Type '''VMD npt.gro''' at the terminal prompt.
+Windows users must first open '''VMD'''.
 Press '''Enter'''.
@@ Line 87: / Line 91: @@
 |  | The molecule '''npt.gro''' gets loaded.
 |  | This is the starting structure file for the '''MD''' simulation of the protein.
 |-
@@ Line 127: / Line 129: @@
 |-
 |  | In the '''Load Files for''' pulldown, choose the '''npt.gro''' molecule.
-|  | In the '''Load Files for''' pulldown, choose the '''npt.gro''' molecule.
+|  | In the '''Load Files for''' pulldown, choose '''npt.gro'''.
 |-
@@ Line 255: / Line 259: @@
 |-
 |  | Hover over '''trajectory''' step and duration.
-|  | Now, the '''trajectory''' step is 1 and movie duration is 4 seconds now.
+|  | Notice, the '''trajectory''' step is 1 and movie duration is 4 seconds now.
 I will retain the defaults.
@@ Line 273: / Line 277: @@
 |-
 |  | Open the '''firstmovie.mpg''' file.
-|  | Open the '''firstmovie.mpg''' file.
+|  | Open the '''firstmovie.mpg'''.
 I will use '''VLC''' media player for it.
@@ Line 342: / Line 346: @@
 |  | Say I want to display, 1st, 49th and 100 th frame only.
-In the form, type, '''1 and 49 and 100''' and press '''Enter''' as seen.
+Type, '''1 and 49 and 100''' and press '''Enter''' as seen here.
 |-
@@ Line 366: / Line 370: @@
 Click on '''Ok''' and then on '''Load'''.
-Close the Window.
+|-
 |  | Close the representations Windows.

@@ Line 43: / Line 43: @@
 [https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
-|  | To follow this tutorial, * Learner must be familiar with basics of '''VMD'''.
+|  | To follow this tutorial,
 * For pre-requisite tutorials, please visit this site.