Daniel R. Roe

I tried V6.24.0 which is bundled with Amber24 and it also worked, so maybe try that. I still recommend using the GitHub version if it's convenient for you though as...

In addition to imaging, the `autoimage` action performs centering (the anchor molecule is placed in the center of the box by default and all other molecules are adjusted accordingly); I'm...

Sorry, I think I didn't understand what your issue was initially. Try adding the `bincenter` keyword for one of the DX files and see if that gives you the result...

> Question: does this affect the computed GIST energies and entropies, or is it just a visualization thing? Nope, it's a visualization thing; basically are you plotting things at the...

> . My DNA is 70 bp long, but I do get as amount of major grooves around 64, which is way too much compared to my DNA strand. The...

> The CPPTRAJ (the code that pytraj uses on the back-end) manual describes how the `nastruct` command determines base pairing: ``` Base pairs are determined either once from the rst...

Sorry for the delay. I've been traveling the past few days and have no laptop (I'm writing this on my phone). That looks OK. I don't think you need to...

Hi, sorry this fell off my radar. The situation at where I work has been difficult the past few months so my response time is way down. I'm having some...

> I think cpptraj does not treat the assignment of groove width to base-pair steps in a proper way. Do you have an instance where CPPTRAJ is not assigning the...

> @drroe how is Jenkins used nowadays in cpptraj? It seems the build keeps failing in this. The failure was unusual (a `std::bad_alloc`) and I have made some under-the-hood changes...