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

Hi,
I am Dr. Dweipayan Goswami,
Welcome to my RUclips 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 :
github.com/DweipayanG/GROMACS...
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
• EP 10 | Protein-Ligand...
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
• EP 1 | MOLECULAR DOCKI...
Other important videos available in the Playlist :
• Bioinformatics-Unplugged

[@JQ-rf1xb]

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

[@davebruno218]

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

[@945corleone]

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 RUclips platform. For this reason, thank you endless thanks.

[@DweipayanG]

Thank you for the support and acknowledging my work

[@lotfibourougaa6209]

Thank you very much...

[@sanjaisrao484]

Learn to ease, ths name is perfect for your channel

[@sanjaisrao484]

Thank you very much
Keep uploading

[@chemistryforall-bynsridhara]

Thank you sir for the valuable tutorial

[@rahulnaga5010]

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

[@drusamaraza4287]

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

[@sanghyunhwang1297]

Thank you so much sir

[@DweipayanG]

😊

[@chemistryforall-bynsridhara]

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

[@user-ev3bo8lw7e]

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?

[@DweipayanG]

Yes !!

[@user-xl4vu9oh1k]

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.

[@DweipayanG]

Agree 💯

[@sanjaisrao484]

Can you please provide all the output files, please