Gromacs/C2/Installation-of-Gromacs-on-Windows-OS/English
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 Number6
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 forWindows subsystem for Linux.
Click on Ok. |
TheWindows Features dialog box opens.
Scroll down and check the box forWindows Subsystem for Linux. Click on Ok. |
Click onRestart Windows. | The system gathers the required information.
A prompt appears asking the user toRestart Windows. Click onRestart Windows, to complete the updates. |
TypeMicrosoft store in the search form and pressEnter. | AfterWindows has restarts, open theMicrosoft store. |
Typemicrosoft store in the search form. | Typemicrosoft store in the search form.
The microsoft store window opens. |
Typeubuntu 20.04 LTS in the search form. | Typeubuntu 20.04 LTS in the search form.
The desired app is the first search result for me. |
Click onubuntu 20.04 LTS icon. | Click on it to see the details. |
Scroll down and click on blue colouredGet button.
If prompted, click onNo, Thanks. |
Scroll down and click onGet to install theUbuntu 20.04LTS app.
|
Close theMicrosoft store. | Allow the process to be completed.
|
Press theWindows key, typeUbuntu 20.04LTS. | Press theWindows key, typeUbuntu 20.04LTS and notice theUbuntu app. |
OpenUbuntu 20.04LTS. | 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 pressEnter. | The very first time, user is prompted to enter a new user name.
I will type my name and pressEnter. 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 pressEnter. | In theterminal enter the command as seen to update the library links.
Allow the process to complete. |
PressCtrl+L. | I will clear the screen for clarity. |
Type,sudo apt-get upgrade and pressEnter. | In theterminal enter the command as seen toupdate the library links. |
Enter the sudo password. | Enter the sudo password if prompted.
Allow the process to complete. |
PressCtrl+L. | I will clear the screen for clarity. |
Type,sudo apt-get upgrade and pressEnter. | In theterminal enter the command as seen to upgrade the library links.
Again, allow the process to complete. |
PressCtrl+L. | Again, I will clear the screen for clarity in the video. |
Type,sudo apt-get install -y build-essential make cmake gcc and pressEnter.
Enter the sudo password if prompted. |
Next, issue the command as seen here.
Enter the sudo user password if prompted. |
Allow the process to be completed.
These processes take time. Make sure to watch the messages for any errors. | |
PressCtrl+L. | Again, I will clear the screen for clarity. |
Type,mkdir gromacs and pressEnter. | Next, create a directory namedgromacs using the command seen here. |
Type,cd gromacs and pressEnter. | Let’s change to the newly created directory. |
Type,wget[1]https://ftp.gromacs.org/gromacs/gromacs-2021.2.tar.gz and pressEnter. | Enter the command as seen, to download the gromacs tarball for installation. |
Type,tar -xvf gromacs-2021.2.tar.gz and pressEnter. | Extract the files from tarball with the command as seen here. |
The files get extracted to a new directory as seen here. | |
PressCtrl+L. | I will again clear the screen for clarity. |
Type,cd gromacs-2021.2 and pressEnter. | The files get extracted to a new directory as seen here.
Let’s change the path to the newly created directory as seen here. |
Show thegromacs-2012.2 folder in the file manager. | For me this particular path is in theDownloads folder inWindows. |
For you it may be different. | |
Type,vim INSTALL and pressEnter. | TypevimspaceINSTALL to open the file invim text editor. |
Show installation instructions. | Scroll down the file using page down or down arrow key.
Detailed stepwise commands to installGromacs 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 startGromacs 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. |
PressCtrl+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 for clarity in the video. |
Typels and press theEnter. | Now enter the commandls to list the files in thebuild directory. |
Show the filesin thebuild directory. | Notice the several files and directories created here.
|
Typecd bin and pressEnter. | Change to the bin directory withcd space bin command. |
Typels and press theEnter. | List the files and notice the gmx executable here. |
Typecd ~ and press theEnter. | Enter the command cd space tilda to go to the home directory. |
Type whereis gromacs and press ‘’’Enter’’’.
to check if files are in /usr/local/gromcs/ directory. |
Please list the files andusing the command as seen here.
Gromacs may get installed inusr local gromacs directory. Check if it is in this directory for you. |
Note down the path of installation. | |
Typevim .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 pressEnter 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. |
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 pressEnter. | 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. |
Typegmx 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, 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 user sudo password if prompted
|
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. |