James McDonagh

3 Questions 12 Answers 0 Followers

Questions related from James McDonagh

How do I calculate the RMSD of a bond length over an MD trajectory?

I am writing a code to calculate the RMSD of all bond in a molecule over an MD trajectory. I am wondering how is best to express/summarize the results. My immediate thought was RMSD, however, I...

10 October 2015 7,238 9 View

Is there an easy way to define the phonon k point list by hand in CASTEP?

Using materials studio to build a CASTEP input for a DFPT phonon calculation, the phonon k point list is built automatically and the calculation follows from a geometry optimisation. As I don't...

10 October 2013 2,547 1 View

Has anyone used upack (Utrecht Crystal Packer)? If so is there a simple reference document for the atom codes and their meaning?

I have been reading through the extensive manual for upack which is generally very helpful but am having difficulties interpreting what all of the atom codes refer too. Is there another document...

01 January 2013 764 0 View