lipid_unwrap.py

[krb0073]

Hi Alan, I placed the lipid_unwrap.py code that I have been working on in loos/Pacakges/Pyloos. Let me know anything that you need me to do and thank you again for all of your help. This code is used ofr simulation that hav rectaulgar boxes to unwrapp the P.B of the simulation. This should work for any selection but is intended to work for lipids. There is one assumption that the lenght of the P.B. is no greater than 1000 which should be fine for most systems. (I could add in a flag to change this if needed). I am also unsure about the change from outputting the x,y,z of each lipid center into the raidus of each point to the center of mass. If you rather have it in the x,y,z for the output I do still have a version of that code. My thinking whne doing that is that now all the points takin in the mostion of the center of mass of the system. Let me know what you need done. Kyle

[agrossfield]

This is connected to Discussion #61

[krb0073]

Alan, Thanks for all the help, it's really nice to get feed back on what I can do to imporve my coding. I removed the comments that were not relavent after pulling everything to the find_fix function, the length function just as well as doing the math by hand, line 232 was modified to have the user choose if they want it to be recentered (defults to yes), and line 259 was fixed by using a 2D martix of size (number of lipids , number of frames). I was wondering if we should do the M.S.D also in this code since the matirx is already in memory?

Kyle