Molecular Dynamics Simulation on GPU ONLINE using GROMACS by Google Colab for totally FREE

This is the easy tutorial of Molecular dynamics Simulation by using GPU ONLINE through Google Colab. Molecular dynamics is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system.

[CricketUpdates]

Thank you Dr Muzammel Rahman for the comprehensive tutorial on MD using GROMACS. I have gone through the tutorial till the end and it was very helpful, indeed. One thing I noticed at the end is, that you forgot to combine the two commands together i.e., printf "proteins" | gmx xxxx x x x x x x xx x x xxx.. You just forgot to add " | " to your code. If you had added this the code would have worked correctly.

Anyhow, the session was nice and I understood many things from this tutorial. Great work.

[ansariiqrar]

Dear Muzzammel Rehman sir, very very thanks for such informative video

[hawazi-svcf]

Alhamdulillah thanks professor, very informative video

[alakanseoluwaseun]

Thanks so much for the privilege to learn, am grateful in person. Can you please do a tutorial on protein_ligand complex MDS also?

[poojadhulap]

how to do the MD simulations for 10 ns in gromacs? and also how to check that it has run for 10 ns?

[farhanazhwinmaulana-]

Very informative video, thanks a lot Mr. So by using this online platform, there is no necessity of installing the gromacs software into our personal computer, right?.

[FFTIME]

Dear Dr you shared a very valuable tool to do simulation but could you please let me know why some commands are not working should we buy access of LGPU or what ?

[yogeshyogi]

Sir did we need to install gromacs everytime we use colab...

Or is it enough to install single time?

[anshumansahu]

Can you say from your experience how much time does collab resources require to run a 100 ns simulation.

[euphoriaplusmovies]

My challenge with MD simulation using Gromacs is conducting it for simulated Ligand-Protein Complex (results of molecular docking studies).
It always seems easier when direct ligand-protein complex from RCSB website is used.

Errors such as Unknown ligand begins to shoot up.

[ulisesdzib]

Muchas gracias señor, que dios se lo multiplique

[حنان.]

Thank you 🙏 but i thin you forgot tom mention how to svae all that especially the code

[anuvyas-vddj]

I have query about MD simulation. How long take time to run the 100 ns MD simulation in google colab?

[mobasserhosain]

sir how long GROMACS can be run in colab ? what is maximum ns can be run ?

[euphoriaplusmovies]

In the file shared, have you already installed the necessary files?

[marcd.]

Greeting will this command works for gromacs 2024.1 and the new cmake 3.28.4?

[MinautiTiwari]

Can I perform this on my laptop? No matter the configurations?

[MuhammadMinhalRaza]

sir also make tutorial for protein ligand complex simulation of uploaded protein complex own

assalamu alikum sir, i got called processerror when installing gromac . what do i do.

[mobasserhosain]

Sir is it possible to used AMD RX580 gpu for gromax ?