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Sulstice2 OP t1_ix6ei5p wrote

Reply to comment by No-Farm6409 in [OC] The Most Common Atoms and Bonds in the Virtual Chemical Universe by Sulstice2

https://en.wikipedia.org/wiki/CHARMM

Look under the section Force Fields for the Potential Energy Function. This predicts the potential energy by iterating through all the atoms and other features of molecules to predict how much energy is available to the system.

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No-Farm6409 t1_ix6myr9 wrote

How is predicting potential energy connected to simulating life?

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Saint_Oliver t1_ix7y3k5 wrote

Electronic potential energy is basically the physics behind chemistry, and biology depends on chemistry.

I will say that potential energy surfaces of molecules are many many steps away from macro biology and maybe far away from cellular biology as well, but personally my knees start shaking when molecules have more than three atoms (biology is not my field).

That being said you can definitely talk quantitatively about potential energy surfaces for things like amino acids. It’s just that, as things get more complex, the tool no longer fits the job and the tools of organic chemistry are more tailored to describe things like protein folding.

I don’t know what OP is talking about btw stimulating life and stuff, but the CHARMM program seems like a legit quantum chemistry program although I’m unfamiliar. It DEFINITELY makes approximations to reach any results as from a physics standpoint molecules are many body problems that do not have exact solutions. The art in science is really making the best approximations you can.

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Sulstice2 OP t1_ix8enbd wrote

CHARMM was awarded the Nobel Prize for being The software for Molecular Mechanics.

It isn't however a quantum chemistry package. I use Psi4 for that.

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Saint_Oliver t1_ix9pz5e wrote

Very cool. It seems tailored for protein folding kind of calculations maybe? Way out of my comfort zone frankly.

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Sulstice2 OP t1_ixau5zz wrote

It's actually for something called van der waals force if you have ever heard of it. It links to my thesis project or will eventually.

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Sulstice2 OP t1_ix8eivb wrote

Molecules interact with each other and they prefer to be in a specific orientation or geometry that is the most energetically favorable. Whatever takes the least amount of work. The equation helps us determine that by separating the energy into different components of physical and electronic characteristics.

In a Force Field we start off small with simple molecular systems and then apply it to larger systems in predicting how atoms will move based on their energy.

So for example, the energy interactions and orientations we use for simple alcohols or carboxylic acids can be applied to lipid membranes and simulating them.

Does that make sense?

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