![]() ![]() You can't normally model shifts of covalent bonds either since that involves changing the molecular composition which breaks the forcefield definitions. It's far from perfect - you usually can't match all measurable physical properties of a medium like water at the same time with the same forcefields. In practice, empirical forcefields are matched to experimental data and molecules are essentially modelled by summing the forces on each atom and using $F=ma$, then integrating the acceleration over time. Molecular Dynamics is currently implemented by making certain approximations in that electron motion is not explicitely modelled. It most certainly exist outside secret labs :) Like Gerben wrote, the fields are called molecular dynamics (MD) and quantum chemistry which, as computers grow faster, will be essential tools of nanotechnology and medicine.
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