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Hello,
This is my first time ever using molecular dynamics simulations and I have to interpret results that I can’t understand. I’ve spent the past hour just trying to understand what does U-B mean and the difference with bond… I wouldn’t even know where to start.
Please I’m in need of enlightenment .
Hi,
This tutorials might help you to understand more on molecular dynamics, force field and GROMACS.
\Alessandra
Thank you, I couldn’t find why is there a difference of energy for bond and u-b but the method is clearer now. Thank you for this ressource
I always interpreted these as bond being the term with all the bonds and U-B being the term with all the Urey-Bradley terms, but I might be wrong.
The second plot is just a distance, which looks super stiff, probably a bond? The relative histogram is basically a single bin because the binning is very large (in terms of the length oscillations) and so you have only ~one occupied state.
Hello, that’s what a I thought for U-B but kept arguing with IA which was telling me non sense.
For the distance, it was measured for 2 cysteins so yes it might be a bond.
Thank you so much for your time !
Hi,
If it helps, you find how Urey-Bradley potential are implemented and how also different bond potential are implemented in GROMACS.
