Difference between revisions of "Gromacs/C2/Installation-of-Gromacs-on-Windows-OS/English"
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Revision as of 11:15, 16 September 2021
| Visual Cue | Narration |
| Slide Number 1
Title Slide |
Welcome to the tutorial on Installation of Gromacs on WIndows 10 OS. |
| Slide Number 2
Learning Objectives |
In this tutorial, we will learn to,
|
| Slide Number 3
Learning Objectives |
* Test the installation with the help command
Installation may take a few hours depending on the hardware. |
| Slide Number 4
System and Software Requirement |
To record this tutorial, I am using
|
| Slide Number 5
System and Software Requirement |
* 64-bit architecture and 4GB RAM or higher are must for the installation
|
| Slide Number 6
Pre-requisites |
To follow this tutorial, * Learner must be familiar with basic computer skills. |
| Slide Number 7
Download Link http://www.gromacs.org/ |
The official website of Gromacs is shown here.
The software is available for Linux and Windows OS. |
| Open web browser and go to | Open a web browser and go to the Gromacs website. |
| Click on the Downloads section in the left panel. | Click on the Downloads section in the left panel. |
| Hover mouse over downloaded here in the right panel and click on it. | The web page is being redesigned at this time.
Click on the downloaded here. |
| Hover mouse over Current Release Candidate.
Click on the Download link below. |
Click on the Download link seen below. |
| Cursor next to Current Release Candidate. | When you practise this tutorial, the version number may be different. |
| Hover mouse over ftp and http download options. | A new page may open with a welcome message for some users.
Under the Source code section, notice the ftp and https options. I will note down the ftp address for later use. |
| Press the Windows key. | Let’s first set up a Linux environment in Windows.
Press the Windows key on the keyboard. |
| In the search form, type control panel and press Enter. | In the search form, type control panel and press Enter. |
| Scroll down theControl panel and click on Programs and Features. | Scroll down theControl panel and click on Programs and Features.
For some of you it will be called Programs. A Programs and Features window opens. |
| In the left panel, click on Turn Windows Features on or off. | In the left panel, click on Turn Windows Features on or off. |
| Scroll down and check the box for Windows subsystem for Linux.
Click on Ok. |
The Windows Features dialog box opens.
Scroll down and check the box for Windows Subsystem for Linux. Click on Ok. |
| Click on Restart Windows. | The system gathers the required information.
A prompt appears asking the user to Restart Windows. Click on Restart Windows, to complete the updates. |
| Type Microsoft store in the search form and pressEnter. | After Windows restarts, open the Microsoft store. |
| Type microsoft store in the search form. | In the search form, type microsoft store and open it.
The microsoft store window opens. |
| Type ubuntu 20.04 LTS in the search form. | Type ubuntu 20.04 LTS in the search form.
The desired app is the first search result for me. |
| Click on ubuntu 20.04 LTS icon. | Click on it to see the details. |
| Scroll down and click on blue colored Get button.
If prompted, click on No, Thanks. |
Scroll down and click on Get to install the Ubuntu 20.04 LTS app.
|
| Close the Microsoft store. | Allow the process to be completed.
After the app is installed,close the Microsoft store. |
| Press the Windows key, type Ubuntu 20.04 LTS. | Press the Windows key.
Type Ubuntu 20.04 LTS and notice theUbuntu app. |
| Open Ubuntu 20.04 LTS. | Click on it to open it.
Notice the initializing message. |
| It will take some time to complete the process. | |
| Type a user name of choice and press Enter. | The very first time, user is prompted to enter a new user name.
I will type my name and press Enter. You may enter your name. |
| Cursor on password prompt. | Next, the prompt asks for a password. |
| Enter a password of your choice and reconfirm it. | Enter your choice of password and reconfirm it in the next step. |
| Press Ctrl+L. | Now the user account setup is complete.
I will clear the screen for clarity. |
| Show Properties option in terminal. | I will increase the font size for clarity, using the properties option.
You may also do so, if desired. |
| Type, sudo apt-get update and press Enter. | In the terminal enter the command as seen to update the library links.
Allow the process to complete. |
| Press Ctrl+L. | I will clear the screen for clarity. |
| Type, sudo apt-get upgrade and press Enter. | In the terminal enter the command as seen to update the library links. |
| Enter the sudo password. | Enter the sudo password if prompted.
Allow the process to complete. |
| Press Ctrl+L. | I will clear the screen for clarity. |
| Type, sudo apt-get upgrade and press Enter. | In the terminal enter the command as seen to upgrade the library links.
Again, allow the process to complete. |
| Press Ctrl+L. | Again, I will clear the screen for clarity in the video. |
| Type, sudo apt-get install -y build-essential make cmake gcc and press Enter.
Enter the sudo password if prompted. |
Next, issue the command as seen here.
Enter the sudo password if prompted. |
| Show installation of library messages seen on the screen. | Allow the process to be completed.
These processes take time. Make sure to watch the messages for any errors. |
| Press Ctrl+L. | Again, I will clear the screen for clarity. |
| Type, mkdir gromacs and press Enter. | Next, create a directory named gromacs using the command seen here. |
| Type, cd gromacs and press Enter. | Let’s change to the newly created directory. |
| Type, wget[1]https://ftp.gromacs.org/gromacs/gromacs-2021.2.tar.gz and press Enter. | Enter the command as seen, to download the gromacs tarball for installation. |
| Type,tar -xvf gromacs-2021.2.tar.gz and press Enter. | Extract the files from tarball with the command as seen here. |
| The files get extracted to a new directory as seen here. | |
| Press Ctrl+L. | I will again clear the screen for clarity. |
| Type, cd gromacs-2021.2 and press Enter. | The files get extracted to a new directory as seen here.
Let’s change the path to the newly created directory with the cd command. |
| Show the gromacs-2012.2 folder in the file manager. | For me this particular path is in the Downloads folder in Windows.
For you it may be different. |
| Type, vim INSTALL and press Enter. | Type vim space INSTALL to open the file in vim text editor. |
| Show installation instructions. | Scroll down the file using page down or down arrow key.
Detailed step-wise commands to install Gromacs is given here. |
| Type, :q! and press Enter. | To quit the text editor, first type colon followed by q! and press Enter.
The command is visible at the bottom left of the screen. |
| Type, mkdir build and press Enter. | Next, create a new directory called build with the mkdir command. |
| Type, cd build and press Enter. | Change the path to the newly created build directory as seen here. |
| Type sudo cmake .. -DGMX_BUILD_OWN_FFTW=ON and press Enter. | To start Gromacs build, enter the command as seen here. |
| Press Ctrl+L. | Allow the process to be completed.
I will clear the screen for clarity in the video. |
| Type sudo make and press the Enter. | Next, type sudo space make and press the Enter key. |
| Show the build process on the screen, | All these processes take time.
Please be patient and allow them to complete. Watch for any error messages. |
| Press Ctrl+L. | Again, I will clear the screen for clarity in the video. |
| Type sudo make install and press the Enter. | Enter the command, sudo make install and press the Enter key. |
| Press Ctrl+L. | With this step the installation process for gromacs is completed.
I will clear the screen again for clarity in the video. |
| Type ls and press the Enter. key. | Now enter the command ls to list the files in the build directory. |
| Show the files in the build directory. | Notice the several files and directories created here.
|
| Type cd bin and press Enter. | Change to the bin directory with cd space bin command. |
| Type ls and press the Enter key. | List the files and notice the gmx executable here. |
| Typecd and press the Enter key. | Enter the command cd to go to the home directory. |
| Type whereis gromacs and press ‘’’Enter’’’.
to check if files are in /usr/local/gromcs/ directory. |
Note down the path of installation using the command as seen here.
Gromacs may get installed inusr local gromacs directory. Check if it is in this directory for you. |
| Type vim .bashrc and press theEnter. | Let’s edit the dot bashrc file with the command seen here. |
| Scroll to the bottom of the file. | Scroll down to the bottom of the file with the page down or by using the down arrow key. |
| Press the Insert key. | Go to edit mode by pressing the Insert key on the keyboard. |
| Use the arrow key and press Enter to start a new line.
Type,alias gmx='/usr/local/gromacs/bin/gmx' |
Start a new line at the end and type the alias for gmx as seen here.
Use the path where Gromacs is installed in your computer. |
| Cursor on the alias line. | Learners must enter the path of the gmx file. |
| Press the Esc key. | Press the Escape key to exit the edit mode in vim. |
| Type :wq and press Enter. | To save and exit, type colon w q without whitespace and press Enter. |
| Typesource .bashrc and pressEnter. | Let’s source to the updated .bashrc file as seen here. |
| Type gmx help grompp and press Enter. | Next, test the installation with the gmx help grompp command as seen. |
| I don’t see any errors in the output.
This shows, that we have installed Gromacs. | |
| Slide Number 8
Alternate installation method |
For alternate installation method, do the following.
|
| Slide Number 9
Alternate installation method |
* Enter the command, sudo apt-get upgrade
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| Slide Number 10
Software Version |
* The latest version of the software may not get installed with this method
|
| Slide Number 11
Summary |
Now let’s summarize. In this tutorial, we
|
| 'Slide Number 12
Assignment |
For assignment activity, please do the following.
|
| Slide Number13
Spoken Tutorial Project |
This video summarises the Spoken Tutorial Project.
Please download and watch it. |
| Slide Number14
Spoken Tutorial workshops |
We conduct workshops using spoken tutorials and give certificates.
Please write to us. |
| Slide Number 15
Forum for questions |
* Please post your timed queries in this forum. |
| Slide Number 16
Acknowledgment |
Spoken Tutorial Project is funded by MoE, Government of India. |
| This is Rani from IIT, Bombay. Thank you for joining. |
