Dear All,
I am trying to perform MSD calculation, which requires me to unwrap trajectory to get continuous behavior. I can not use built-in ‘gmx msd’ for my case. Apparently, gromacs’s trjconv offers multiple options to accomplish the task. I tried followings (2 ways),
• First approach, Make starting frame whole using ‘-pbc whole’, followed by ‘-pbc nojump’.
• Second approach, Using ‘-pbc whole’, followed by ‘-fit progressive’
To my understanding, I should get same msd from both approach, but I don’t.
Could someone help me understand, what does ‘-fit progressive’ do that leads to different unwrapping than ‘-pbc nojump’. And, what is the right approach to unwrap trajectory for dynamic properties?
Sincerely,
Masrul Huda