I am interested in calculating the x,y and z distance between two molecules over a given simulation time. I know how to calculate the total (r) distance between them, but I want the distance between them along all three dimensions.
For the total distance, cpptraj can be used as:
parm prmtop-file trajin netcdf-file distance DIST :1-4@heavy-atoms-from-molecule-1 :5-8@heavy-atoms-from-molecule-2 out dist.out run quit
But like I said before, I do not want the r-distance. Is there anyway to calculate the x,y and z-distances in cpptraj? If not, what other alternatives do I have?