Decoding Molecular Dynamic Simulation steps - What do the GROMACS Tool Commands mean?
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- Опубликовано: 9 сен 2024
- Gromacs is a tool for carrying out Molecular dynamics in Linux. Understanding the Linux commands help us to troubleshoot Gromacs MD simulations. Inthis video we decode the Molecular Dynamic simulation steps and try to understand the GROMACS TOOL.
About the Lecturer:
Prof. Sanket Bapat completed his Ph.D. from the premiere CSIR-National Chemical Laboratory and the Biotechnology and Bioinformatics Institute, Pune. He worked as a project fellow in Haffkines Institute of Training, testing and Research, Mumbai where he worked on identifying target proteins in Swine Flu. Along with knowledge of statistical and biochemical techniques, he has also published several research papers in peer-reviewed journals and written a book chapter to his credit. Apart from research, he has a strong background in academic and institutional teaching experience.
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Hello everyone, There are some sections in this video where my camera has frozen, but the commentary and video is perfect and has no lag. The topic can still be understood.
Thank u sir it is really helpful please make a video on creating a personal ligand database.
@@sameerqureshi1178 what is personal ligand database means?
Sir thank you for this video..But during running of NPT step I am getting an error regarding some PME rank...I am not understanding how to solve this? Kindly help me
I am a crystallographer, learning bioinformatics through your videos. Really need to master docking and simulation for a project.
Thank you very much for the video on simulation commands, helped a lot to understand the commands as well as for troubleshooting
Thank you for making this video, it's been really helpful!
Super great! this is the greatest explanation for newbie
Sir u r a savior seriously , ❤️ thankyou so much.🙏
Thank a lot. Really appreciable
WOW, AWESOME TEACHING SIR. Thank you so.........much
wow awesome teaching sir. thank you very much
Thank You for making these videos on MD simulations. Please make video regrading the analyzing results of gromacs.
Hello sir, thanks a lot for this video it was really informative and I have one request can you please make some videos on analysis of MD simulation please sir. It would be great if you could consider this, thank you sir!...
I have explained the RMSD, energyand RMSF graphs in the video
Thank you for making this video. It will be very helpful if you make a video on protein-protein complex simulation
very helpful video and very well explained plz upload more videos on charrm force field
Amazing video
Thank you, this video helps a lot !!!
Thank you
hi sir
How does one extend the protein simulation in Gromacs ?
50ns finished and i want to extend it to another 50ns ? thanks in advance.
Sir can you explain the concept of periodic boundary
Fatal error:
Residue 3 named GLN of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
please how do I solve this error issue
thank you so much sir
decoding the MD simulation of protein - ligand
Nicely explained!
Thank you for this good vedio
I am getting error - File 'minim.mdp' does not exist or is not accessible. pls can you help
really helpful, thank you!!
Thank you so much for this detailing video. it's really really helpful. In the same way, Could you make the analyzing results (RMSD, RMSF, hbond, binding energy)videos if possible!!
While running the final step of MD, I am getting this error "40 OpenMP threads were requested. Since the non-bonded force buffer reduction is prohibitively slow with more than 32 threads,", My server can handle 20 cores. Can you help me, how can I reduce the number of core to be used?
Are you using GPU?
@@sanketbapat No sir
Ohh you are using server, i did not read that setence. Specify 18 cores, don't utilize the full Number of cores.
@@sanketbapat Yes sir, that's what I am asking, can you share how to specify the number of cores I want to use? That would be a great help.
@@sanketbapat Hello Sir, I have fixed the problem, I am sharing it here in case if you want to know it. The core count to be used has to be mentioned at the end, for example like this, gmx mdrun xxxx -ntomp yy, where yy = the # of core I need to use. Thanks again :)
very useful info tqsm
Thank you. God bless
It is great! !!!
Sir I can't adding solvent in topology file can u help?
Sir please make a video on this topic how we do simulation for the micelle of surfactant molecule in gromacs
tnx alot sir
In which step do we fixed the number of molecules of protein and water and also the value of temperature and pressure?
Hello sir, thank you very much for your work, it's very informative. I have two questions tho: 1) why isn't there a position restraint in the last step of building a complete md_0_1? 2) how can one calculate how much time in reality will be spent on building a simulation of for example 1 ns? I would very appreciate if you could answer or recommend me sources in which I could learn this. Thanks!
Sir, Can you explaim why in some of the simulations we need both CG models and Atomistic models and how can we simulate both these models??
where the heating and cooling is done , and how to set values for that
Hello sir. Thanks for your vedios. But I have a small doubt. This vedio is for protein before docking. But I want to know how to do simulations for protein-ligand complex after docking
Check protein ligand docking MD simulation video on my channel
It was very informative sir . Can U please help me how to create residue topology database for Zn ?
Plz make i video on analysis of protein ligand interactions through MD simulations
I have made it, check the playlist.
Can you make tutorial for free energy perturbation for drug free energy prediction? Many thanks.
Hi Sanket! Great work. Can you please make a FEP tutorial for drug receptor complex? That would be a great help.
I have uploaded a video of molecular dynamic simulations for protein-drug
@@sanketbapat yes I've seen that, really commendable. Thank you so much for that. FEP is an advanced topic of course, if you can make one tutorial for FEP, that would be great.
Greetings
Your videos are extremely helpful for bioinfo students.. Can you suggest me how can I do simulation at different pH..How can I write a command for ions, box n all.
Thank you, Check the mdp files for changing the pH. You can check my videos on how to perform MD simulation.
@@sanketbapat I thought we just have to prepare the protein at different protonation states but use the same mdp file?
Hello sir can you make a video on MD simulation or protein-receptor complex on gromacs? I need to simulate a vaccine-receptor complex simulate can you please help me? I will grateful to you. I have to start my MD Simulation learning on Gromacs by watching your video. I have learned a lot. Nicely explained sir. Thank you very much.
Check the Molecular Dynamics Playlist, there is a video on Protein MD simulations, check if that helps.
@@sanketbapati find protein-ligand simulation I learn from that but I am looking for protein-protein simulation. Is it the same way like protein-ligand simulation?
Sanket tumhi punyache ahat ka?
Yes