Basics of Molecular Dynamics Simulations for Beginners

This video introduces the very basics of molecular dynamics (MD) simulations—the most popular technique to simulate the dynamics of atoms and molecules. We review the concepts of interatomic potential (energy of interaction between atoms) or forcefield, molecular dynamics iterative algorithm, time discretization, and numerical integration.

[mehtashirley]

I have taken a course on Basic Simulations and this really helped me, your explanation was far more better than at my university. Helped me alot.

[khaled-ikez]

This was an amazing video. thank you! I just wanted to make sure that everything I know is right or not.

[LeeZhenYong]

After going through a lot of convoluted material on this subject, this video is a breath of fresh air.

[purvaashtri]

Was very helpful to get an insight into what molecular dynamics is. Eager to see more such videos. :)

[MrThrenorius]

Perfect sir ! The most useful video on MD for noobies, so far :)

[jiangxu]

This introduction is concise and clear!!! Thumb up !!!

[hashrafi]

sometimes we know how to run a simulation but don't know what we are exactly calculating. this simple video is great!

[omermutasim]

This is pure Gold ! . Very informative, Thanks a lot

[cajusammon]

Could you make a video explaining (Mesh) Ewald Summation, which seems to play a big role in MD?

[SreeramPeela]

Nice and simple presentation. Thanks for sharing your knowledge with us..wish there were videos on deeper concepts..

[atalvats]

This was actually a very lucid way of explaining this topic! Loved it!

[rezamoosavi]

great explanation! God bless you, Mat!

[newtonihoeghian]

Very useful video, teaches the theory behind the simulation with so much ease

[nabarunr]

This was so well explained. I was having a hard time understanding it by reading only. Thank you.

[aliciascience]

Thank you so much for this lucid and concise introduction!

[FarzadMohaddes]

I really enjoyed your explanation of the MD cycle around min 20. Thank you.

[cmlnm]

Thank you very much for the course, which is very informative for me as a beginner.

[CoconutSundae]

Wonderfully explained, thanks so much for making this for us!

[annaliesemeyer]

Clear and comprehensible introduction!

[FunHah]

Fanstastic explanation, but I think there is a mistake (or I did not get it probably). The first force you calculated was a derivative of energy with respect to distance but the starting structure at t=0 has the atoms at a constant equilibrium distance (for instance an energy minimized structure). So without first taking a step (t = 0 you said), the force will be zero. If it is otherwise, however, it means you have taken arbitrary step to compute the force. Please let me know what you think. Thank you