this is a great video, sir. it has helped me more than you know. i wish the best to you
@BioinfoCopilot
Ай бұрын
Thank you 🙏
@Jaeoh.woof765
8 ай бұрын
4:45 : PDB 5:05 : Charmm Force Field 6:05: ChimeraX 8:22 Charmm Gui 13:18
@BioinfoCopilot
8 ай бұрын
Thank you
@assimverma8746
Жыл бұрын
Thak you so so much for this video. It helped me alot in understanding the basics of md simulation. Please upload the next part of it to make us understand the step by step guide to generate rmsd graph of protein and protein+ligand.
@BioinfoCopilot
Жыл бұрын
Thank you. Yes here it is : kzitem.info/news/bejne/yZluwIyYiH92maw
@boorasanjit2013
2 жыл бұрын
Thank you so much for this video, I learned so much.
@BioinfoCopilot
2 жыл бұрын
Thanks and welcome 🙏🏼
@arijitsamanta3660
11 күн бұрын
Sir if I want to change the simulation run time length, do I change the steps only in the mp.mdp file or other mdp files too?
@BioinfoCopilot
11 күн бұрын
You have to change in the mdp file and then you can start it from the point where the simulation is done. Remember that you have to use grompp to generate new files and then run the simulation.
@alishaandmom
9 ай бұрын
Hello, Thanks for your fantastic video. Could you please make a video on how to do coarse grain MD simulation using CHARMM force field and GROMACS? Thanks in advance!
@BioinfoCopilot
9 ай бұрын
Thank you 🙏. Yes definitely 👍
@swatideshmukh7708
Жыл бұрын
Oh.. i think many more people are using gromacs in uppsala uni.... coz,when im searching for gromacs md on protein , seen two diva thesis. Well, as said by Dr.Justin on tutorial page, we have to edit few parameters. But you havent done. Is it ok to deal with the given mdp as it is????
@BioinfoCopilot
Жыл бұрын
Yes, you can proceed with the default mdp file as long as you are dealing with proteins. GROMACS is developed here at Uppsala.
@pppcat
2 ай бұрын
are you sure? In the gromacs webpage they suggest to modify the default parameters to use the charmm force field
@BioinfoCopilot
2 ай бұрын
Depends on what you want to achieve! Well sometimes the default parameters works in my case if only I am dealing with the protein system only.
@vpanagiotou481
9 ай бұрын
excellent video!! could you please sir continue making videos for this md tutorials lemkur page asap please ?!!
@BioinfoCopilot
9 ай бұрын
Sure absolutely. Thank you 🙏
@MashiDani
8 ай бұрын
Please share how to use gromacs for peptide membrane which has made by charmmgui
@BioinfoCopilot
8 ай бұрын
Sure will do! Thanks
@kuldeepsharma4376
Жыл бұрын
Sir please make a video on this topic how we do simulation for the micelle of surfactant molecule in gromacs
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