Alex Izvorski

Hi @flaport - Thanks, that's really helpful! I'm still slightly confused by "simulation units" :) There may be two different interpretations (which may be equivalent, maybe) (a) the equations are...

@flaport "instead of power we should just define a electric field amplitude" - I like this, it's intuitive. It seems that the point/line sources convert power to amplitude and then...

@flaport Thanks, very cool! I'm going to try specifying a point dipole with known amplitude and see if the detected power vs distance in the far field matches the expected...

@flaport Thanks for explaining, good to know that these are new quantities with new units. I think I'm getting close to actually understanding this :) > This means that the...

> From what I'm understanding by reading this, I'm assuming one can convert E from simulation units to V/m by simply dividing the simulation units by √ε0 and H_sim to...

@flaport Thank you for the excellent explanation - I hope this is useful to anyone who has the same questions in the future. Indeed mostly resolved. How do you feel...

> The gradients are available at every step, however since they are a rather large vector we so far refrained from printing them along the optimization trajectory. > > What...

@awvwgk It seems that'd be less efficient, double the compute even with restarting. Let's say 100 steps to optimize a structure, then 100 single point calculations with gradient - vs...

@ShahbazQalandar The base tip3p.xml doesn't have any ions included, but the version amber14/tip3p.xml does. The simple fix is to use `app.ForceField('amber99sbildn.xml', 'amber14/tip3p.xml')`. Despite the name that wouldn't include anything else...

@peastman Was thinking of having a shot at this as it is needed to get OPC ions, any feedback before I get started on it?