Gromacs/C2/Creating-Input-Files/English - Revision history

Snehalathak at 05:44, 27 October 2021

2021-10-27T05:44:43Z

Ranipv076 at 11:50, 26 October 2021

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Ranipv076 at 11:39, 26 October 2021

2021-10-26T11:39:02Z

Snehalathak at 11:16, 26 October 2021

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Snehalathak at 11:15, 26 October 2021

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Ranipv076 at 16:59, 24 October 2021

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Ranipv076 at 16:58, 24 October 2021

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Ranipv076 at 16:56, 24 October 2021

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Ranipv076 at 16:56, 24 October 2021

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Ranipv076: Created page with " {| border=1 || '''Visual Cue''' || '''Narration''' |- || '''Slide Number 1''' '''Title Slide ''' || Welcome to the spoken tutorial on '''Creating Input Files'''. |- || '''..."

2021-10-21T14:00:24Z

Created page with " {| border=1 || '''Visual Cue''' || '''Narration''' |- || '''Slide Number 1''' '''Title Slide ''' || Welcome to the spoken tutorial on '''Creating Input Files'''. |- || '''..."

New page

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

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

'''Title Slide '''
|| Welcome to the spoken tutorial on '''Creating Input Files'''.

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

'''Learning Objectives'''
|| In this tutorial, we will learn about,
* Flow chart to setup a MD run for a protein in a solvent box
* Delete water molecules present in the starting pdb file
* '''pdb2gmx''' command and syntax
* Generate .'''gro''' and '''.top''' files

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

'''Learning Objectives'''
|| * About force field and selecting a force field
* Generate the '''topology''' file
* '''editconf''' command

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

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

* '''Ubuntu Linux''' v20.04 OS
* '''Firefox''' web browser v92
* '''gedit''' 3.36
* '''Gromacs''' v2021.2

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

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org] '''
|| To follow this tutorial,
* Learner must be familiar with basic computer skills.
* 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.

|-
|| Open a web browser and go to [https://manual.gromacs.org/archive/5.0/online/flow.html https://manual.gromacs.org/archive/5.0/online/flow.html] .
|| Open a web browser and go to the '''Gromacs''' link as seen here.

The flow chart here, shows the procedure for '''MD''' and data analysis.

|-
|| Cursor on the flow chart.
|| I will demonstrate parts of this procedure till the addition of a bounding box.

|-
|| Press '''Ctrl''', '''Alt''' and '''T''' keys together.
|| Open a '''terminal''' by pressing '''Ctrl''', '''Alt''' and '''T''' keys together.

'''Windows''' users can open the '''Ubuntu''' 20.04 '''app'''.

|-
|| Type '''mkdir firstmd''' and press '''Enter'''.
|| Type '''mkdir space firstmd''' to create a new directory.

|-
|| Type '''cd firstmd''' and press '''Enter'''.
|| Change path to the newly created '''firstmd''' directory with the '''cd''' command.

|-
|| Open the '''File Manager'''.
|| Open the '''File Manager''' and go to the '''firstmd''' directory.

|-
||
|| Let’s consolidate all our input files here.

From now on, I will not mention this separately.

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

'''FIle path for Windows Users'''
|| * '''Windows''' users must find the path of this directory in '''Windows'''.
* Detailed instructions are provided with the tutorial.
* Use this path when locating, opening or moving files, which are saved to here.

|-
|| Copy '''1AKI.pdb''' to the '''firstmd''' directory.
|| Copy the provided '''1AKI.pdb''' input file to this directory.

|-
|| Open the '''1AKI.pdb''' file in a text editor.
|| Open the '''1AKI.pdb''' file in a text editor.

|-
|| Scroll to the end of the file.
|| Scroll to the bottom of the file.

In many files downloaded from the '''PDB''' website, water molecules will be present.

|-
|| Show water molecules '''HOH''' from '''1AKI.pdb''' file.
|| They are denoted as '''HOH''' and present at the end, before the model ends.

|-
|| Highlight the '''HOH''' from '''1AKI.pdb'''.
|| If so, be sure to delete them and save the file, before proceeding further.

|-
|| select all the '''HOH''' containing rows molecules and delete them.
|| Let’s select all the lines starting with '''HOH''' molecules and delete them.

Lysozyme is well studied, stable and a model protein.

Hence we will also use it for learning the steps of protein '''MD''' for beginners.

|-
|| Show absence of '''H''' atom in the file.
|| Notice that hydrogens atoms are absent in this structure file.

We will not add them.

The '''Gromacs''' commands will add the hydrogens for the user later on.

|-
|| Save the file and quit the text editor.
|| Now, save the file and quit the text editor.

|-
||
|| Structures determined by '''NMR''' methods may not contain the water molecules.

|-
|| Annotation: '''Windows''' users use appropriate path in your system.
|| Let’s learn a few '''terminal''' commands to generate input files for '''MD'''.

|-
|| Type '''gmx pdb2gmx -f 1AKI.pdb -o first.gro''' .
|| All the commands start with the phrase '''gmx''' which calls '''Gromacs'''.

Enter the commands as seen and retain the syntax.

|-
|| Highlight '''pdb2gmx'''.
|| The second word tells '''Gromacs''', what command is to be performed.

Here, it is '''pdb2gmx''', which will convert the '''pdb''' file to '''gro''' file input file format.

|-
|| Highlight '''-f 1AKI.pdb '''.
|| The '''hyphen f''' flag denotes the input file and it is '''1AKI.pdb'''.

|-
|| Press '''Enter'''.
|| The '''hyphen o''' flag refers to the output file and I will name it '''first.gro'''.

Press the '''Enter''' key and we will enter an interactive mode.

|-
|| Cursor on the force field and publication details selection.
|| Selection of '''force field''' and '''solvent''' addition is interactive in this command.

First, several forcefieds are listed, for the user to pick from.

|-
|| Cursor on the details page.
|| The details off publication for each of the '''force field''' is also listed.

To learn further, learner is referred to the publication listed.

|-
|| Type '''4''' as seen here and press the '''Enter''' key.
|| Learner must know their system to select the number for the desired force field.

'''Lysozyme''', is a protein without unnatural modifications.

Hence I want to select '''AMBER94'''.

To select '''AMBER''', type '''4''' as seen here and press the '''Enter''' key.

|-
|| Cursor and highlight the response on the '''terminal'''.
|| Gromacs returns the force field that will be used as '''amber99.ff'''.

By convention, '''.ff''' denotes '''force field '''files and the path of file is also seen.

|-
|| Highlight solvent environment options.

Type '''2''' and press '''Enter'''.
|| Next, the user is prompted to add a water model to the system.

Type '''2''' for '''tip4p''' and press the '''Enter''' key.

|-
||
|| Sometimes, users desire for different solvent system to be added.

If so, create a '''topology''' file and add it to the library.

|-
|| Show file manager with the newly created files.
|| Open the file manager and notice the newly created files.

|-
|| Cursor on the file manager showing the newly generated files.
|| Three files, with '''.gro,''' '''.top''' and '''.itp '''extension are created with this command.

'''.top''' is the topology file and '''.itp''' is include topology file.

|-
|| Open '''first.gro''' in text editor.
|| Let’s open the generated '''first.gro''' file that gets created in a text editor.

Notice that, this command has also added hydrogens to the file.

|-
|| Cursor on 4-6 columns.
|| The 4th, 5<sup>th</sup> and 6<sup>th</sup> columns are the atomic coordinate positions of the atom.

|-
|| Close the '''firstmd.gro''' file.

Press '''Ctrl+L'''.
|| Let’s close the '''firstmd.gro''' file.

I will clear the '''terminal''' screen for clarity in the video.

|-
|| Show '''Gromacs''' manual website on '''getting started'''.

[https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup https://manual.gromacs.org/archive/5.0.4/online/getting_started.html#setup]
|| Learner may go through the '''Gromacs''' website on '''getting started'''.

The link is shown here.

|-
|| Type '''gmx editconf -f first.gro -o box-added.gro -c -d 1 -bt cubic'''.
|| Next, enter the '''editconf''' command, which adds a solvent box to the system.

This is to define the volume where the simulation will be performed.

'''Editconf''' does not create a new conformational state for the protein.

|-
|| Cursor on '''-f''' and '''-o''' flag.
|| This command also generates '''.gro''' file like the '''editconf''' command.

Again '''-f''' denotes input file and '''-o''' denotes output file.

|-
|| Type''' -c '''.
|| Cubic and hexagonal shapes are popularly used for the bounding box.

The '''hyphen c''' flag places the center of the molecule in the center box.

|-
|| Type''' -d 1 '''.
|| The''' -d''' flag denotes distance from the

center of the box to the boundary.

Here 1 denotes 1nm, which is half of the length of the box.

Increasing the box size will considerably lengthen the '''MD''' run time.

|-
||
|| If using '''lysozyme''', the max length for '''lysozyme''' can be of the order of 90 A.

So the box length is a little bigger than the molecule under study.

|-
|| Type''' -bt cubic '''.
|| Next, enter the shape of the box, which I will enter to be of cubic shape.

If another shape is desired, use the '''-bt''' flag with the shape name.

|-
|| Press '''Enter''' to run the command.
|| Let’s run the command.

This generates another input '''.gro''' file, with box size and sets file names.

|-
|| Cursor on the details.
|| The box volume that is created is displayed in cubic nanometers.

|-
||
|| The extent of shift of the coordinates is also mentioned in nanometer.

|-
|| Show screenshot of''' box-added.gro'''.
|| Let’s open the '''box-added.gro''' in a text editor.

Notice that, the coordinates have shifted to accommodate aligning in the box.

|-
|| Close the text editor.
|| Learner may pause the video, and explore the options further.

Close the text editor window.

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

'''Summary 8'''
|| Now let’s summarize. In this tutorial, we learned about,

* Steps in a '''MD''' run for a protein in a solvent box
* The '''pdb2gmx''' command and syntax
* About adding a force field
* Generated .'''gro''' and '''.top '''files

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

'''Summary 9'''
||
* About '''editconf''' command
* Define the size of a bounding box
* Set the position of the molecule in the box

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

'''Assignment 10'''
|| For assignment activity, please do the following.
* Use a '''PDB''' ID of another protein of your choice.
* Practice the commands learnt in this tutorial.
* Read publications of your choice which use '''Gromacs'''.

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

'''Assignment 11'''

'''http://www.mdtutorials.com/gmx/'''
|| * Go to the website seen below.
* Choose a tutorial of your choice and read it

|-
|| '''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 138: / Line 138: @@
 || Let’s select all the lines starting with '''HOH''' molecules and delete them.
-Lysozyme is a well studied, stable and model protein.
+Lysozyme is a stable, well studied model protein.
 Hence we will also use it for learning the steps of protein '''MD''' for beginners.
@@ Line 148: / Line 148: @@
 We will not add them.
-The '''Gromacs''' commands will add the hydrogens for the user later on.
+The '''Gromacs''' commands will add the hydrogens for us.
 |-
@@ Line 160: / Line 160: @@
 |-
 || Annotation: '''Windows''' users use appropriate path in your system.
-|| Let’s learn a few '''terminal''' commands to generate input files for '''MD'''.
+|| Let’s learn a few '''terminal''' commands to generate the input files for '''MD'''.
 |-
@@ Line 191: / Line 191: @@
 || Selection of '''force field''' and '''solvent''' addition is interactive in this command.
-First, several force fieds are listed, for the user to pick from.
+First, several force fields are listed, for the user to pick from.
 |-
 || Cursor on the details page.
-|| The details off publication for each of the '''force field''' is also listed.
+|| The details of publication for each of the '''force field''' is also listed.
 To learn further, learner is referred to the publication listed.
@@ Line 205: / Line 205: @@
 '''Lysozyme''', is a protein without unnatural modifications.
-Hence I want to select '''AMBER99'''.
+I want to select '''AMBER99'''.
-To select '''AMBER''', type '''4''' as seen here and press the '''Enter''' key.
+To select '''AMBER''', type '''4''' and press the '''Enter''' key.
 |-
 || Cursor and highlight the response on the '''terminal'''.
-|| Gromacs returns the force field that will be used as '''amber99.ff'''.
+|| '''Gromacs''' returns the '''force field''' as '''amber99.ff''' that will be used .
-By convention, '''.ff''' denotes '''force field '''files.
+By convention, '''.ff''' extension denotes '''force field '''files.
 The path of the file is also seen.
@@ Line 230: / Line 230: @@
 || Show output and total charge of the system.
 || In the output notice the total charge on the system listed.
-Learner is encouraged to pause the video and explore more on the solvent addition.
+Learner is encouraged to pause the video and explore the solvent addition.
 |-
@@ Line 240: / Line 240: @@
 || Three files, with '''.gro,''' '''.top''' and '''.itp '''extension are created with this command.
-'''.top''' is the topology file and '''.itp''' is include topology file.
+'''top''' is the '''topology''' file and '''.itp''' is '''include topology''' file.
 |-
@@ Line 258: / Line 258: @@
 || Let’s close the file.
-I will clear the '''terminal''' screen for clarity in the video.
+I will clear the '''terminal''' for clarity in the video.
 |-
@@ Line 270: / Line 270: @@
 |-
 || Cursor on '''-f''' and '''-o''' flag.
-|| This command also generates '''.gro''' file like '''pdb2gmx''' command.
+|| This command also generates '''.gro''' file like before '''pdb2gmx''' command.
 Again '''-f''' denotes input file and '''-o''' denotes output file.
@@ Line 276: / Line 276: @@
 |-
 || Type''' -c '''.
-|| Cubic and hexagonal shapes are popularly used for the bounding box.
+|| The '''hyphen c''' flag places the center of the molecule in the center box.
-−
 The '''hyphen c''' flag places the center of the molecule in the center box.
 |-
@@ Line 284: / Line 282: @@
 || The''' -d''' flag denotes distance from the center of the box to the boundary.
-Here 1 denotes 1nm, which is half of the length of the box.
+Here 1 denotes 1 nm, which is half of the length of the box.
 Increasing the box size will considerably lengthen the '''MD''' run time.
@@ Line 296: / Line 294: @@
 || Next, enter the shape of the box, which is cubic.
-If another shape is desired, use the '''-bt''' flag with the shape name.
+If another shape is desired, use the '''bt''' flag with the shape name.
 |-
@@ Line 304: / Line 302: @@
 Cubic and hexagonal shapes are popularly used for the bounding box.
-This generates another input '''.gro''' file, with box size and file name.
+This generates another input '''gro''' file, with box size and file name.
 |-
@@ Line 312: / Line 310: @@
 |-
 ||
-|| The extent of shift of the coordinates is also mentioned in nanometer.
+|| The extent of shift of the coordinates is also mentioned.
 |-
@@ Line 318: / Line 316: @@
 || Let’s open the '''box-added.gro''' in a text editor.
-Notice that, the coordinates have shifted to accommodate aligning in the box.
+Notice that, the coordinates have shifted to accommodate aligning with the box.
 |-
@@ Line 339: / Line 337: @@
 * Steps in a '''MD''' run for a protein in a solvent box
 * The '''pdb2gmx''' command and syntax
-* About adding a force field
+* About adding a '''force field'''
 * Generated .'''gro''' and '''.top '''files
 * About '''editconf''' command

@@ Line 37: / Line 37: @@
 * '''Ubuntu Linux''' v20.04 OS
 * '''Firefox''' web browser v92
-* '''gedit''' 3.36
+* '''gedit''' v3.36
 * '''Gromacs''' v2021.2
@@ Line 82: / Line 82: @@
 |-
 || Type '''cd Documents''' and press '''Enter'''.
-|| '''Linux''' users can change directory to Documents using the cd command as seen.
+|| '''Linux''' users can change directory to '''Documents''' using the '''cd''' command as seen.
 |-
 || Windows users may skip this step and remain in '''home''' directory.
 || Windows users must create this directory first.
-Hence, type '''mkdir Documents''' before changing path with '''cd''' command.
+Hence, type '''mkdir''' space '''Documents''' before changing path.
 |-
@@ Line 112: / Line 112: @@
 |-
 || Copy '''1AKI.pdb''' to the '''firstmd''' directory.
-|| Copy the '''1AKI.pdb''' file input file to this directory.
+|| Copy the '''1AKI.pdb''' input file to this directory.
-For Windows users this path is likely to be in C drive.
+For Windows users this path is likely to be in C drive and in the user system folder.
 |-

@@ Line 95: / Line 95: @@
 |-
 || Type '''cd firstmd''' and press '''Enter'''.
-|| Change path to the newly created '''firstmd''' directory.
+|| Change directory to the newly created '''firstmd''' directory.
 |-

@@ Line 82: / Line 82: @@
 |-
 || Type '''cd Documents''' and press '''Enter'''.
-|| '''Linux''' users can change directory to Documents using the cd''' command as seen.
+|| '''Linux''' users can change directory to Documents using the cd command as seen.
 |-

@@ Line 1: / Line 1: @@
-{border=1
+{|border=1
 || '''Visual Cue'''
 || '''Narration'''

@@ Line 100: / Line 100: @@
 || '''Slide Number 7'''
-'''FIle path for Windows Users'''
+'''File path for Windows Users'''
-|| * '''Windows''' users must find the path of this directory in '''Windows'''.
+||
 * Detailed instructions are provided with the tutorial.
 * Use this path when locating, opening or moving files, which are saved here.
@@ Line 190: / Line 191: @@
 || Selection of '''force field''' and '''solvent''' addition is interactive in this command.
-First, several forcefieds are listed, for the user to pick from.
+First, several force fieds are listed, for the user to pick from.
 |-
@@ Line 365: / Line 366: @@
 '''http://www.mdtutorials.com/gmx/'''
-|| * Go to the website seen below.
+||
 * Choose a tutorial of your choice and read it.

@@ Line 24: / Line 24: @@
 '''Learning Objectives'''
-|| * About selecting a force field
+||
 * Specifiy the size and shape of bounding box for MD
 * '''editconf''' command
@@ Line 335: / Line 336: @@
 '''Summary 8'''
 || Now let’s summarize. In this tutorial, we learned about,
 * Steps in a '''MD''' run for a protein in a solvent box
 * The '''pdb2gmx''' command and syntax