Basics of Molecular Dynamics Simulations for Beginners

[@amalinasabri1850]

The best explanation I could get for understanding what's happening during the molecular dynamics simulations

[@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.

[@niamcd6604]

If I may, *far better. NOT far more better.

[@khaled-ik1ez]

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

[@jessesonnenschein5665]

This talk is simply brilliant, you have saved my life, thank you 🍀

[@LeeZhenYong]

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

[@MrThrenorius]

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

[@omermutasim1200]

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

[@jiangxu3895]

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

[@newtonihoeghian8155]

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

[@hashrafi7148]

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

[@nabarunr3]

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

[@Nabarun_Dawn]

Hmmmm

[@purvaashtri]

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

[@cmlnm]

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

[@SreeramPeela]

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

[@MBauchy]

Many thanks

[@cajusammon1170]

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

[@rezamoosavi71]

great explanation! God bless you, Mat!

[@atalvats]

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

[@annaliesemeyer2830]

Clear and comprehensible introduction!

[@aliciascience]

Thank you so much for this lucid and concise introduction!

[@Farzad1982Mohaddes]

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

[@CoconutSundae]

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

[@payalwadhwa7993]

Wonderful lecture, Thank you very much!!!

[@Ericlau1126]

Its very straight forward and easy understanding! Thanks for your teaching!

[@amitimsc]

A quick intro to MD. Thank you.

[@chidozienwanedo9234]

Thanks for this explanation. really helped

[@mazenhamdan2424]

thank you it was really useful. I would like to learn more about MD

[@dr.rajeevamp3487]

Nice presentation on molecular dynamics simulations sir

[@nagabhushanabr8479]

Thanks for this special presentation.

[@vinaykumar-ed2jq]

Very helpful information..Thanks for your effort..

[@gabco11]

C'était très clair, tu gères ! Merci :)

[@maxheiderscheid8658]

Thanks a lot for this awesome video! perfectly explained!

[@dr.rameshbhise2178]

Excellent presentation. Thanks a lot!

[@peterlauridsen8403]

Love it - thank you very much

[@kuanliangshao5997]

Great videos! Thank a lot. But sometimes hard to read your handwriting.

[@zhangbruce6007]

yep

[@hassanahmadsheikh5130]

How the hell he was able to deliver all of this and I mean simply its dope.

[@itsnaturescience1433]

Thank you very much for such a simple explanation....

[@MBauchy]

Many thanks

[@maratusoleha7682]

Thank you its usefull and clear explanation

[@bonbonpony]

17:23 Although slightly better (cuts the number of calculations by two), it's still of the QUADRATIC order. Is there any better way of calculating interactions between particles than going through each pair one by one? I know that this could be done for collision detections, by subdividing space in a recursive way (e.g. octrees or K-D trees) and excluding all those pairs that are too far away to be able to collide, but I don't see how the same trick could be applied to forces, since they can still act even at large distances :/ (sure, we can neglect all those interactions for atoms that are too far away and the force of interaction is negligible), but I don't thing that would make the cut. Are there any better ideas?

[@Flash_345]

That's about it really. You make an approximation and only calculate interactions upto a certain cutoff. For the vDw terms this gives very small errors as the value decays fast with respect to distance. For electrostatics, you divide the interactions into two parts, where the short range interactions are calculated directly from the equation in the video, but the long range interactions are determined from the Fourier transform of real space. Check out the methods titled, "Ewald summation" or "Particle mesh ewald".

[@sachin271093]

Thank you. Helpful to understand the basics

[@MBauchy]

Many thanks, thanks for watching!

[@Mohamedshehata]

If anyone is interested in protein modelling and molecular dynamic simulations , you may refer to my channel I teach the basics of VMD program which is used widely in molecular dynamic simulations and protein structure analysis kzbin.info/aero/PLhYF9QNr23IaG-aFub24_T8XnIbJb7fNU

[@ankitsinghnegi3587]

Got sparked ! Want more on that topic.

[@omarh9410]

Thank you very much, very helpful and useful.

[@MBauchy]

Many thanks!

[@kkm5384]

Good video. Tahnks. got some basic idea of MD simulation. and the direction of accelaration is decided by the Force vector. right?

[@SaltedEgg_MiaMiaMia]

Thank you very much! Very useful explanation!

[@WeallMaharashtra]

Nice and informative video.Thanks Sir.

[@gcam474]

Just happened upon this video by chance. I had to move on early in the presentation when you indicated that you must know position and momentum simultaneously at the outset. Forgive me if i missed some bigger concept. Will take my chances though.

[@universaleducationpoint4605]

Thank you for informative lecture.

[@anandarup-bnk]

Thanks for a great video. Just one query. Isn't Coulombic interaction inversely proportional to the square of the distance of separation? You haven't mentioned power of 2.

[@MBauchy]

Santanu Roy Thanks for watching! Coulombic energy decreases as 1/r, and correspond force decreases as 1/r2.

[@anandarup-bnk]

@@MBauchy Oh yes, sure. How stupid of me.

[@raqshiqishraaq8740]

life saver...thanks a lot...plzz keep more videos coming

[@MBauchy]

Thanks!

[@gayatriprasad3790]

Good video presentation.

[@ahmeds4]

Would I need a solid understanding of quantum mechanics to excel in this area?

[@FCommentary]

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

[@loigiap6082]

wow, great video, hope you keep uploading videos. Thanks a lot!

[@MBauchy]

Thanks!

[@MohammadAli-rk7sr]

Thanks alot. great video for beginners

[@amjadkhan-sj9iw]

Very well explained

[@mehuldave6839]

Amazing video sir

[@mairavidal1722]

Great video! Thank you so so much!

[@hemantkumarmeshram7304]

great explanation!!

[@Mohamedshehata]

Perfect , waiting more videos like this ..please go on

[@MBauchy]

Thanks for watching!

[@sharifulislam-tj2dy]

Great video!

[@BSardine]

Thanks so much, this was very helpful.

[@MBauchy]

Thanks for watching!

[@AnkitCuhp]

❤ great explanation!!

[@drbinus1064]

Very informative session.

[@xabixam]

Very nice explanation. However, I have always wondered why initial velocities are required when setting up a MD simulation? Does the energy of the system (and the resulting forces on the atoms) also depend on the initial velocities?

[@balaram4967]

xabier arias yes in reality initially in fluids every particles is moving with some velocity because only at absolute zero temperature atoms or molecules won’t have any moment... rest of the cases they have finite momentum

[@xabixam]

@@balaram4967 True! thanks for the reply

[@zy9662]

I think in depends. For example if you're simulating just one protein molecule then every atom in the molecule may be started at velocity zero, because at the beginning of the simulation you don't have any idea of the velocity of each atom

[@dr.lathan7263]

Nice session

[@md.abdullahalhasan595]

thank you.... please upload tutorial videos of molecular dynamics simulations in LAMMPS

[@MBauchy]

Check out this video: kzbin.info/www/bejne/h5XcmJyYgrxkd6s

[@kkm5384]

Thanks a lot for simplistic explanation of the concept. Now i have some queries. between 28:33 to 29:06 you mentioned different positions of the atoms. But where in the direction of motion is changing? which parameter is reflecting about that direction? Though its denoted as vector, i am still not clear about how this is being taken care and in what way? Wish to have a reply from you or anyone, please. Happy new year.

[@niki6399]

THANK YOU FOR THIS!!!

[@rsphysics2646]

Thank you for information

[@enachaki]

its an amazing video.

[@dr.ashwindesaibm7711]

wonderful

[@raqshiqishraaq8740]

plzz upload a video discribing the statistical mechanics needed for molecular dynamics

[@MBauchy]

Please subscribe to the channel to receive the future videos from our group.

[@manis2k9]

thank you very much

[@disitiazolamida]

Fantástico!!!

[@meenus5458]

Thank you

[@ياسمينعزيزة-ح2ر]

you are great thanks

[@Potentflowconsult]

Thank you sir!!!

[@oktawiuszraczynski5174]

It's great video

[@maninikovatrouvski5391]

just amazing thank's

[@ameerkhazal1458]

Actually very useful, big likkkkkke

[@fitchem11]

Hi there. keep it up a great work.

[@MBauchy]

Thanks for watching!

[@fitchem11]

@@MBauchy Hi! may i know are you researcher/scholar or molecular modeler?

[@fitchem11]

Tq Dr . :)

[@edthoreum7625]

MD 15:14

[@surajitmandal8225]

Interesting.

[@priyadeshwal6848]

🙏...

[@EndureTemptation]

Your ones are [A]mazing

[@chinnayanbright9480]

Good

[@ItsMe-yb1zn]

❤❤❤❤❤❤❤❤❤❤❤❤❤❤

[@Afreenkhan-fh3fu]

wow!!!!!!

[@ivan_wang]

Damn, too many ads

[@lt.arvinddhurve626]

Thank you so much for this lucid and concise introduction!

[@goutamkumarmaity4815]

Thank you very much! Very useful explanation!

[@salaheddinesb7312]

thank you very much, the explanation was great

[@jayashreebagawade696]

Thank you for informative lecture.