Webinar Demonstration - Molecular Dynamics Simulation of Protein-Ligand using Gromacs

Learn using Gromacs for Protein-Ligand Molecular Dynamics Simulations and running basic analysis using VMD

[harshitatiwari]

This is the most comprehensive tutorial on MD simulation in youtube so far.

[koyel]

this is so informative and really helped me a lot while I was looking for GROMACS tutorial from scratch with proper understanding.. thank you Jitesh.

[RABUCHANGMAI]

I am new to MS. I watched a lot of tutorials. This is the Best one...

[sajedatunnesa]

The way you provide basics and explain every little details is really extraordinary👌👌

[uttaranbhattacharjee]

Your presentation really helpful. Thank you and best regards.

[janasalamonova]

Hello, would you be so kind and provide us with the slides? when you were talking about the files (49:00 - 56:00) we could not see it :(

[rikniranjanmukherjee]

it was a very helpful session. please keep making such content. please make more videos on gromacs (other chemical systems, their analysis, and free energy and trajectory-based calculations).

[memunasaqib]

i am new in this field but i must say you are doing great job . please update your channel and make more content..

[anishamanchanda]

Thank you so much for such a nice and helpful presentation sir

[ES-ydze]

The command that ordered to calculate rmsd between ligand and protein by vmd in tutorial is
protein or resname K23 is that true
Please anyone correct me

[gahinde]

Sir can you please recommend the system requirements like processor, ram, hdd, graphics card, ssd for operating GROMACS🙏🏻

[karthickeyan]

my protein have zinc ion and hydroxide ion. i tried all type of forcefield but i could not run simulation it shows error zn residues not found or oh residue not found. did you have any suggestion for run my protein.

[ramakrishnamacharyach]

I also trust you shall make an elaborated video on MM PBSA/GBSA methods by using gromacs files because many a time peer reviewers are insisting to perform these calculations. Thanks

[mathivel]

There were two group entries for K23 at 2:20:47 such as 13 and 19. Why you selected K23 (19) over K23(13) ?

[PharmaAI-LearningCenter]

Hi, I want to run simulation on GPU but I am unable to configure GPU during Gromax installation. Basically Gromax is not detecting my GPU. On other side, I am using Desmond on same system and there is no any issue in performing simulation. Please guide me about how to configure GPU on Gromax.

[ASTUDIO-official]

a beutifull talk and welldone program at that leavel . thank you for that kind of concepts

[shivampandit]

Thank you for such a insightful session professor, it will be really helpful if you can show us how to perform MMPBSA BFE calculations using Gromacs for the complexes

Thank you in advance

[ketan]

how to set forcefield for Zn because it is not supported by the general forcefields and external
softwares?

[SwaraGTheGardener]

Hi sir, I am receiving error after adding the force field, could you help me why it is coming my molecule has only carbon and hydrogen atoms.

[hanstsahnang]

Awesome presentation. Please which command line can you use to launch the production step on GPU and CPU simultaneously. Thanks