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.
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 ?
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?.
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 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 .
@@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..
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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.
Dear Muzzammel Rehman sir,very very thanks for such informative video
Thank you brother 🌹
Thank U Dr. Muzammel Rahman..
Alhamdulillah thanks professor, very informative video
I am really so thankful to you..
Thank you. I will make whatsapp group. You can sent an email or you can comment over here
Muchas gracias señor, que dios se lo multiplique
Thanks so much for the privilege to learn, am grateful in person. Can you please do a tutorial on protein_ligand complex MDS also?
Yes sure , i will upload that soon
Thanks so much! Thanks for the privilege!
@@MuzzammelRehman when you upload for tutorial on protein_ligand complex MD for gromacs in goole collab 🙏
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 ?
Nice video Sir
Thank you
very informative, sir.
Thank you brother
Sir did we need to install gromacs everytime we use colab...
Or is it enough to install single time?
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?.
nope
how to do the MD simulations for 10 ns in gromacs? and also how to check that it has run for 10 ns?
Can you say from your experience how much time does collab resources require to run a 100 ns simulation.
Thank you sir
Thanks
I have query about MD simulation. How long take time to run the 100 ns MD simulation in google colab?
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.
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
@@MuzzammelRehman I moved to Taiwan and changed my number
sir how long GROMACS can be run in colab ? what is maximum ns can be run ?
Greeting will this command works for gromacs 2024.1 and the new cmake 3.28.4?
Can I perform this on my laptop? No matter the configurations?
assalamu alikum sir, i got called processerror when installing gromac . what do i do.
In the file shared, have you already installed the necessary files?
yes . The commands for installation is available in file. It takes some time therefore i did not do it in tutorial
@@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 .
sir also make tutorial for protein ligand complex simulation of uploaded protein complex own
what is before bash command, it is not clear.
It is not free. Even when I run it for as little as 10 ns.
really helpful....
Sir is it possible to used AMD RX580 gpu for gromax ?
in my case xmgrace command is not workingg
Sir please how to create drive folder can you please elaborate me
As Salamu Alaikum. Good video. Can you please make one for GROMACS in local pc?
WSWRWB
Yes , In Sha Allah i will upload it soon
Sir, can you elaborate how to upload local .pdb files? Thank you.
great
thank you
bhai 1KAI k ilawa bhi koi use kr lo..... local files k sath kese kr skte wo bhi bta do
Local files can be imported or if you have other pdb then you can replace that id with 1KAI
@@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..
@@a.rakhayaseen5447 follow the step where i uploaded md.mdp file , likewise upload your pdb
Please upload this vedio after wards
What you do mean by this ?
@@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.
Asalamu alaikum sir
Is it free?
GROMACS is free. I’m not sure about Google Colab, though
I am sorry i got you late. Sir, do you have any whatsapp group.
Yes I have
@@MuzzammelRehman sir then kindly share your WhatsApp group