New answers tagged computational-chemistry
7
We can't simulate everything because there isn't enough computing power to do it
The fundamental problem of making chemical predictions is that they are extremely hard to do because of the combinatorial complexity of what needs to be simulated.
Chemists can and do simulate, though. Big computational models can approximate molecular structures and reactions. ...
6
What you have in mind sounds like Molecular Mechanics. Atoms are treated there like classical particles and are simulated using classical physics, including Coulombic forces. But we know that this is not sufficient. Effects like protons tunneling can not be explained within that model, just to name one.
Including all known laws of physics into simulations of ...
9
I wondered why we can't/don't have perfect knowledge about how things work on an atomic level
Well... we do. The things you have suggested (like VSEPR theory) are very crude, though, and not suitable for such tasks. Obviously, if it was a matter of just coding in Coulombic forces, somebody would have done it already.
More appropriately, everything should be ...
5
The actual partition function is unimaginably formidable. For just $N$ point particles in a 3D box, it's already got $3N$ dimensions. If the box is length $L$, GROMACS would probably divide the box into a machine-precision grid and calculate the energy from $\sim L \times 10^{10}$ values in each dimension. The partition function would incorporate all of that ...
0
To use it you would need access. Outside of D.E Shaw Research there is only 1 available ANTON, and you simply can't go out and buy one as far as I can see.
Looking further into the business relationships of David Shaw, it's clear that he is part of Relay Therapeutics (https://relaytx.com/our-team/david-e-shaw-ph-d/) and I wouldn't be surprised if there is ...
2
For any wave function, you can define the one particle density matrix $\int \psi(x_1, \dots, x_n)\psi^\ast(x_1^\prime, x_2, \dots, x_n) dx_2\cdots dx_n$. The eigenfunctions of this operator are single particle functions and are called natural orbitals. For a treatment of reduced density matrices see for instance [this book] (https://www.springer.com/gp/book/...
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