Molecular Dynamics Simulation | Gromacs Installation (Win&Linux)| BeginnerTutorial | Bioinformatics
95,202
Published 2020-09-06
If your have error in installation or other troubleshoot issue join in our Facebook group : www.facebook.com/groups/261045198486665
Instagram : www.instagram.com/bioinformatics.bb/
Molecular dynamics is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system.
Minimum System Requirement
- Intel Core i5 processor
- 16 GB RAM
- 1 TB hard disk
- 4 GB Graphic Card
MD simulations software’s: en.wikipedia.org/wiki/Category:Molecular_dynamics_…
Gromacs: manual.gromacs.org/documentation/
Gromacs Tutorial: www.mdtutorials.com/gmx/lysozyme/index.html
CUDA installation: www.pugetsystems.com/labs/hpc/How-to-install-CUDA-…
GPU installation : www.nvidia.com/en-sg/data-center/gpu-accelerated-a…
Gromacs Installation: manual.gromacs.org/documentation/2019/install-guid…
ions.mdp : bit.ly/3k4LbtF
mini.mdp: bit.ly/3bxIqxD
NVT.mdp: bit.ly/3i3VBJa
NPT.mdp: bit.ly/35anZWz
md.mdp: bit.ly/357XJMx
All Comments (21)
-
amazing work! Couldn't have done it without your tutorial. You broke down such a daunting task in a step by step fashion, thanks a lot!
-
Thank you sir u really helped me to learn molecular dynamics and has beginner it's really helpful ❤️🔥and I nearly watched your nearly 50 to 100 times to learn step by step and part 2 simulation gromacs I nearly watched 50 to 100 times am glad some teachers helped in social media for other students to learn once again thank you sir ❤️🔥💝
-
thank you sir for this valuable tutorial your videos are very clear and easy to understand these helped me alot
-
Thank you very much for your video! Greatings from Germany :)
-
thank you for yiour video SIR, canwe form the topology using Charm-Gui force field for gromacs input?
-
sir, you are doing great in explaining bioinformatics stuff. please make detail video on Drug designing and admet analysis. Thanks alot.
-
Many thanks 🎉🎉for the great work and explanation 👍 😊
-
Great work man. Is there any online tool for converting my .edr files to .xvg for graph visualization?
-
Very interesting Please my question is that can I install both LAMMP and Gromacs at same time in windows?
-
thanks very much for this tutorial
-
The PCA and free energy-based analysis to understand the correlation of atomic movements in the vaccine-receptor complexes and Free-energy based binding energy calculations (MM-PBSA/GBSA).How can i perform both of them??
-
I'm trying to install gromacs with gpu acceleration using WSL2, but running into some errors, have you ever tried it? I really need some help with it
-
Hi sir, I am trying to identify the CHRAMm forcefield of different bases using Discovery studio visualizer, but i am not able to obtain required data from it. can you please help me out of it sir.
-
Sir, is it possible to do molecular simulations for protein-protein complexes? if yes, kindly share the online server and applications for protein-protein simulations
-
Thanks for the tutorial it actually helped me to Install gromacs but immediately I close my terminal , and open it back, as I hit gmx the message which appears on the terminal is "gmx command not found , use sudo apt get install to download the command gmx". Which is not normal as I go the build directory as I hit gmx is still get the same message as cited above what's the real problem since I installed gromacs successfully.
-
Sir if i already installed cuda, gpu and gromacs, how to activating my gou for run my simulation?
-
You are an amazing teacher! I have watched so many of your videos. You have the best explanations and most easy to follow directions. Thanks so much for all your help! One extra help, have you ever done Charmm-gui to gromacs? There is only one video and it is in Spanish:) Thanks for all you do:)
-
Amazing teaching skills. Salute your acumen. However, need some guidance. Stuck at 8:16 moment of this video. Kindly elaborate it a little, how can i find path in my desktop. Gromacs was downloaded by sudo apt-get install gromacs, but i dont know where it has disappeared in the desktop
-
Sir what is minimum hardware requirement for run MD 200ns per day?
-
HI sir, If I runnig a complex simulation, Can I go to my other work with the system at the same time?
