EP 11 | Post MD Simulation movie for visualization Protein-Ligand complex trajectories | Gromacs

Hi,

I am Dr. Dweipayan Goswami,

Welcome to my YouTube channel "Learn at ease"

In this video I have explained how to perform post MD simulation visualization of Protein-Ligand Complex in the from of Video and how to export the video.

# Tutorial, Codes and Files used in this video will be found at Github :

This video is in continuation with my previous video:
EP 10 | A to Z of Protein-Ligand MD Simulation in Gromacs | Reusable commands and files provided

The files of protein ligand complex is the docked complex which I had prepared in my video :
EP 1 | MOLECULAR DOCKING in UCSF CHIMERA by VINA Plugin from Scratch in Linux

Other important videos available in the Playlist :

[JQ-rfxb]

Thank you for your wonderful explanation, it helped me tremendously😁

[corleone]

One of my teachers used to say, "If someone chooses the hard way to teach you something, know that he doesn't know anything." I haven't seen anyone teach better than you on the Youtube platform. For this reason, thank you endless thanks.

[sanjaisrao]

Learn to ease, ths name is perfect for your channel

[rahulnaga]

Sir can u make a video on mmpbsa. Thank you so much sir for this md videos. It is very much useful

[davebruno]

Really you did a fantastic explanation and work. Thank you, sir.

[drusamaraza]

One of best and easiest way to perform MD simulation, thanks for making so east and conceptual detailed video .
I have a question.
That if a drug has mechanism of doing conformation change in protein or denature it so how it can be checked through MD simulation or RMSD or protein stability value kindly elobrate it

[chemistryforall-bynsridhara]

Thank you sir for the valuable tutorial

[BhawnaDixit-sh]

Nice explanation, however, I find that in a lot of tutorials, waters are stretched, the protein is rotating around, does not seem correct, did you treat the PBC (trjconv) and remove rotation and translation because then only a correct trajectory can be visualized. If you calculate RMSD to first frame within this trajectory, it is going to give weird results since you didn't remove rotation and translation.

[MasihuzzamanAnsari-ov]

sir i could not find the MD /ensembled analysis in my tools of chimeraX. please response how i can get that and also is it necessary to have gromacs and chimera in the same system to get that. please reply

[gibsonalbert]

Hi! sir! if I have more than one protein-ligand complex pose, there should be different runs per pose?

[chemistryforall-bynsridhara]

Sir, I have performed a 50ns md simulation, can I extend the simulation to 100ns, if so please guide me
thank you.

[sanjaisrao]

Can you please provide all the output files, please