16

I can't answer in the context of DFT/VASP, where these terms might have specific uses, but I can offer some general comments. These terms are not necessarily mutually exclusive: Total energy probably refers to the combined kinetic and interaction energy $E=K+P...$ resulting from summing/integrating over the whole Hamiltonian. In DFT this would be the ...


11

As I have previously discussed with you, there is no such thing as frame-wise free energies, so the premise of your question is flawed. With this in mind, I think it would actually be useful to tell something about what FEP can do. FEP is used to calculate the free energy difference between two macrostates with corresponding Hamiltonians $H_0(x)$ and $H_1(x)...


11

In principle, you would expect the exact opposite (i.e. explicit better than implicit) simply because an explicit model more closely matches the reality of molecules interacting with other molecules rather than some sort of continuum. In practice, you generally can't achieve full explicit solvation or even a single solvation shell and are limited to working ...


9

From what I have read, the performance of implicit models depends on a combination of the method used (Poisson-Boltzmann vs. Generalized-Born vs. another analytical method); and the size, shape, and species of the solute (ie: protein vs. ion). I think the best way to answer this would be to search for prior work on different solvation methods applied to the ...


8

Generating all possible structures systematically might be difficult. When it comes to the generation and refinement of chemically useful structure guesses, I'd recommend looking into CREST by Stefan Grimme. It will sample your entire structure space, i.e, not only intermolecular docking motifs, but also intramolecular conformations. It uses an MM approach ...


7

Highly depends on what your system of interest is. (i) For molecular and ionic systems, check papers by Chris Cramer and Donald Truhlar. (ii) Another paper of interest for heterogeneous catalysis could be the below paper. Basically for nonpolar/weakly polar solute implicit solvation is pretty good. However, the solvation energies can start to deviate for ...


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