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gradient descent != molecular dynamics; the latter is simulating forces on atoms, not attempting to optimize a target function. You can use molecular dynamics
by natechols 8y ago
gradient descent != molecular dynamics; the latter is simulating forces on atoms, not attempting to optimize a target function. You can use molecular dynamics for optimization too - it can be very powerful, just slow - but I don't think that's what they're describing here.
- electricslpnsld 8y agoI read it as they are using a molecular dynamics package to define a function (potential energy of the protein structure) and are using gradient descent to (slowly) reach stable extrema (static configurations of the protein).
- natechols 8y agoThat makes more sense, but the energy function isn't really a feature of molecular dynamics, anything that does molecular optimization or modeling will have this information built in.
- deleted 8y ago[deleted]
- hmartiniano 8y agoYou're absolutely right. My bad, mixed too many ideas at once :). Gradient descent (or similar techniques) can be used for structural optimization with the same atomistic models used in molecular dynamics.