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By molecular dynamics, I assume you mean molecular dynamics using force-fields (a.k.a. Classical Molecular Dynamics). Remember that there is also ab initio MD. Force fields are parameterised, i.e. they depend on the a set of constant parameters, which have been previously fitted to reproduce experimental data/high level ab initio results. These parameters ...


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"But they cannot handle "exotic" materials. Why?" You have claimed this without a reference! MD in principle can be done for any group of interacting particles, especially if you have an accurate forcefield. The issue is that classical MD with a classical forcefield will probably not do as well for an exotic material like a ...


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If the content of the .cif in question is fairly molecule-like, my recommendation are the cod-tools collection by the Crystallography Open Database. These may be obtained directly from their web site; if you use Debian 10/buster or Ubuntu 18.10LTS and higher, you equally find them in the the repositories (DebiChem tracker). A typical extraction follows the ...


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