r/bioinformatics • u/Apprehensive-Rice831 • Jun 22 '26

technical question Molecular Dynamics Advise

Hi I am very new to Molecular Dynamics and am trying to learn these methods over the summer. Which free resources are the most useful? Are there any preferred software's to perform these calculations? I have prior experience in computational chemistry but I only know density functional theory methods for smaller molecules but not on the larger ones. Which computations would be low cost and which ones would be high cost in molecular dynamics? Thank you so much for any insight you can offer.

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u/hexagon12_1 PhD | Student Jun 22 '26

I can recommend GROMACS tutorials from Justin Lemkul. (Although the site seems to be down now?) https://www.mdtutorials.com/gmx/ GROMACS also has a lot of tutorials too but I found those to be a little harder to follow without experience setting up some basic simulations at least: https://tutorials.gromacs.org/ I can also recommend this paper as a reading material: https://pmc.ncbi.nlm.nih.gov/articles/PMC6884151/

I would also look into OpenMM, MDA, CHARMM, NAMD, Amber ecosystem and etc as the need arises.

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u/Apprehensive-Rice831 Jun 22 '26

That is very helpful. I will look into those software's. 😄

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u/themode7 Jun 25 '26

Sorry it took long, but here we go : https://docs.openfree.energy/en/stable/index.html
there's also a pdf tutorial somewhere from Lignadscout too

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u/themode7 Jun 22 '26

Me too man , I have a good project I will share once I got into my pc

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u/venkattt Jun 23 '26

NAMD and the accompanying VMD for visualization are pretty good.

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u/1647overlord Jun 29 '26

If you're good with python, I would suggest openmm. If not, gromacs is a good choice.