Unwrapping trajectory for MSD calculation

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

Hi Masrul,

I would assume that in case you allow your molecule to rotate during the progressive fit, while in the other case it remains static - thus I would expect that your msd is lower for -fit progressive than for pbc nojump.

Hi Masrul,
I have the same question. Have you solve the problem? I want to know -pbc whole(or -res or mol) & -pbc nojump can get the unwrapping trajectory?
Thank you !
LM

Dear Masrul,
I am new to GROMACS. I would be grateful if you could explain about wrapped and unwrapped coordinates.