Daniel R. Roe
Daniel R. Roe
Pinging @EricChen521 @acruzpr @jokr91 @gosldorf @cnnguyen @tkurtzman since they are the real GIST experts. So as far as I can tell from the code, you are correct and the `Eww-`...
Sorry there hasn't been much movement on this. Unfortunately I haven't had much time for new development over the past few months.
By default, cpptraj will only look for solute-solute hydrogen bonds. If you want to explicitly look at water-water hydrogen bonds, you need to explicitly specify the water donors and acceptors:...
> Is this the complementary similarity used to then find medoids and outliers in the trajectory? Yes - it's equivalent to the `gen_sim_dict` routine from `src/tools/esim_modules.py` in MDANCE.
> gen_sim_dict will take as an input a set of frames/conformations, and output a number (the extended similarity) for the whole set, not a number for every frame. Yes, I...
Hopefully addressed by #259
@swails I'm trying to figure out the intended behavior for SPAM here. I think the "do you want to calculate energy" part was to allow just reordering of the waters,...
> Can remind me again about the real difference between action and command? In the new framework, the core of any command given in cpptraj is the class `DispatchObject`. There...
> But I don't have a good feel for how people are actually using it in the wild. I don't either. A brief search of my email (which includes Amber...