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.
gist.github.co...
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[@CricketUpdates365]

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.

[@ansariiqrar8888]

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

[@MuzzammelRehman]

Thank you brother 🌹

[@alakanseoluwaseun7119]

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

[@MuzzammelRehman]

Yes sure , i will upload that soon

[@alakanseoluwaseun7119]

Thanks so much! Thanks for the privilege!

[@risnawapujiastuti8534]

@@MuzzammelRehman when you upload for tutorial on protein_ligand complex MD for gromacs in goole collab 🙏

[@kashafaltaf3462]

I am really so thankful to you..

[@MuzzammelRehman]

Thank you. I will make whatsapp group. You can sent an email or you can comment over here

[@hawazi-sv4cf]

Alhamdulillah thanks professor, very informative video

[@togetherJHD597]

Thank U Dr. Muzammel Rahman..

[@muhammadasaduzzaman6987]

very informative, sir.

[@MuzzammelRehman]

Thank you brother

[@sreejitsoman8325]

Nice video Sir

[@MuzzammelRehman]

Thank you

[@FFTIME360]

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 ?

[@ulisesdzib8418]

Muchas gracias señor, que dios se lo multiplique

[@farhanazhwinmaulana-1298]

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?.

[@a.rakhayaseen5447]

nope

[@inayatsaidi3872]

Thank you sir

[@MuzzammelRehman]

Thanks

[@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.

[@MuzzammelRehman]

I have text you on your whatsapp number as you removed me from the group so i think my number is blocked on your whatsapp

[@euphoriaplusmovies]

@@MuzzammelRehman I moved to Taiwan and changed my number

[@poojadhulap]

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

[@hashtagpeace]

really helpful....

[@anshumansahu1087]

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

[@yogeshyogi8468]

Sir did we need to install gromacs everytime we use colab...
Or is it enough to install single time?

[@user-it6hj6zs2d]

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

[@A_Writers_Block]

As Salamu Alaikum. Good video. Can you please make one for GROMACS in local pc?

[@MuzzammelRehman]

WSWRWB

[@MuzzammelRehman]

Yes , In Sha Allah i will upload it soon

[@assimverma8746]

It is not free. Even when I run it for as little as 10 ns.

[@euphoriaplusmovies]

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

[@MuzzammelRehman]

yes . The commands for installation is available in file. It takes some time therefore i did not do it in tutorial

[@muhammadriaz570]

​@@MuzzammelRehman sir can you please help me in fixing the error which says no proper dihedral type in .itp file in adding ion steps I am doing MD simulation by gromacs using charmm force field .

[@aalilouyoussra3365]

great

[@MuzzammelRehman]

thank you

[@marcd.8571]

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

[@anuvyas-vd3dj]

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

[@1234567890000918]

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

[@mobasserhosain6916]

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

[@MinautiTiwari]

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

[@sachindhawale2134]

what is before bash command, it is not clear.

[@nitinjain1703]

in my case xmgrace command is not workingg

[@muhammadshahab1421]

Sir please how to create drive folder can you please elaborate me

[@mobasserhosain5446]

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

[@kashafaltaf3462]

Please upload this vedio after wards

[@MuzzammelRehman]

What you do mean by this ?

[@kashafaltaf3462]

@@MuzzammelRehman sir, at that time it was a live session that is why I requested to upload this vedio on you tube. Still a lot of thanks to you sir.

[@zhenwang323]

Sir, can you elaborate how to upload local .pdb files? Thank you.

[@kashafaltaf3462]

Asalamu alaikum sir

[@kashafaltaf3462]

I am sorry i got you late. Sir, do you have any whatsapp group.

[@MuzzammelRehman]

Yes I have

[@muhammadriaz570]

​@@MuzzammelRehman sir then kindly share your WhatsApp group

[@a.rakhayaseen5447]

bhai 1KAI k ilawa bhi koi use kr lo..... local files k sath kese kr skte wo bhi bta do

[@MuzzammelRehman]

Local files can be imported or if you have other pdb then you can replace that id with 1KAI

[@a.rakhayaseen5447]

@@MuzzammelRehman but how to import local files? i tried uploading the file even through drive.... in your provided tutorial i aam facing issue at the downloading steps even i have changed the links..

[@MuzzammelRehman]

@@a.rakhayaseen5447 follow the step where i uploaded md.mdp file , likewise upload your pdb

[@shakilcuchem]

Is it free?

[@a.h.378]

GROMACS is free. I’m not sure about Google Colab, though