Daniel R. Roe

> it's hard to tell if cpptraj is compiled with what `cpptraj --defines` can give you an inkling of what features cpptraj was compiled with; for example, if OpenMP support...

This is a good idea, and one that has been on my agenda for a while. I actually have a branch that does an overhaul of how topology information is...

Great idea @hainm thanks!

> Where are the header files pytraj needs? Does cpptraj put them in $CPPTRAJHOME/include? It should, but it doesn't. I'll have to modify the install process to be something more...

> The changes are in the conda branch at github.com/Amber-MD/cpptraj. There are only two one-line changes to the cpptraj code: adding a missing header in Matrix.h, and changing the location...

So my development process is I have my own fork of Amber-MD/cpptraj: https://github.com/drroe/cpptraj I make my branches from that repository, e.g. https://github.com/drroe/cpptraj/tree/prepareforleap.remote.buildatom When I'm ready, I can make a merge...

In cases where you want to remove global rotational and translational motions, you should definitely align the frames before calculating the mass-weighted covariance matrix. You can do so either by...

Sorry this fell off my radar for a bit. > Should I use all eigenmodes, when I calculate the entropy? So assuming you are referring to the thermodynamics analysis activated...

Hi, sorry for the delay here. I haven't delved into the code yet but my suspicion is that there is an `int` somewhere being used in matrix indexing; max size...

Sorry, for the delay on this; recent issues at my workplace have made things challenging. I should have asked this from the beginning: what version of cpptraj are you using?...