Hi
Does anyone know what the length of a time step is in Avogadro’s AutoOptimization tool?
May we clarify, which version of the program do you use?
Second, do you refer with «Avogadro’s AutoOptimization tool» to the geometry optimization (in Avogadro 1.95.1, either shortcut Ctrl + Alt + o, or (in the GUI), Extensions → OpenBabel → Optimize Geometry)? If this would be the case, than no, there is particular time interval per individual step of optimization.
Note, depending on what you want to do with the optimized structure, you might opt to change the force field used. UFF is pretty old and e.g., MMFF94s is much better for typical small organic molecules (Extensions → OpenBabel → Configure Force Field). On occasion, you will recognize a structure optimized within one set of force field and its parameters is going to change in favour for an other conformation because of changing said parameters of optimization.
If you are interested in background why one optimization algorithm is labelled as «steepest descent», and the other «conjugate gradient», then the youtube channel TMP Chem with its installments about computational chemistry (root entry; the video about steepest descent, and the one about conjugate gradient) might be useful for you.
Or, do you refer to set up/run a MD simulation?
Thanks - I am on the original Avogadro v1.2.0
Yes - I’ve been using the AutoOptimization tool. If there is no particular time interval for each step, then i guess each step represents the same interval then?
I am running MD simulations using a GAFF forcefield.
Well, if you are aiming for a MD simulation, count me out; because so far, I never set up/perform a MD, neither in Avogadro, or elsewhere. The section of the TMP Chem channel mentioned earlier is a reference I currently use to get some understanding about MD (self-study) and the tutos about MD are still ahead of mine. Hopefully Geoffrey Hutchison or an other reader may offer a succinct answer.
While there is an “MD” mode, I wouldn’t take it too seriously. It doesn’t have a rigorous thermostat or timescale. It’s intended more for “let’s show that we can move around on the potential energy surface.”
I’m working on a more rigorous molecular dynamics mode for 2.0.
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