# Unwrapping trajectory for MSD calculation

**URL:** <https://gromacs.bioexcel.eu/t/unwrapping-trajectory-for-msd-calculation/360>\
**Category:** User discussions\
**Created:** [June 22, 2020, 8:41pm UTC](https://gromacs.bioexcel.eu/t/unwrapping-trajectory-for-msd-calculation/360 "2020-06-22T20:41:14Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Masrul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/masrul/32/234_2.png) [@Masrul](https://gromacs.bioexcel.eu/u/Masrul)\
**Post date:** [June 22, 2020, 8:41pm UTC](https://gromacs.bioexcel.eu/t/unwrapping-trajectory-for-msd-calculation/360/1 "2020-06-22T20:41:14Z")

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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

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**Author:** ![cblau](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cblau/32/5_2.png) [@cblau](https://gromacs.bioexcel.eu/u/cblau)\
**Post date:** [June 26, 2020, 3:40pm UTC](https://gromacs.bioexcel.eu/t/unwrapping-trajectory-for-msd-calculation/360/2 "2020-06-26T15:40:58Z")

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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.

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**Author:** ![littlema](https://avatars.discourse-cdn.com/v4/letter/l/b19c9b/32.png) [@littlema](https://gromacs.bioexcel.eu/u/littlema)\
**Post date:** [April 15, 2021, 9:10am UTC](https://gromacs.bioexcel.eu/t/unwrapping-trajectory-for-msd-calculation/360/3 "2021-04-15T09:10:25Z")

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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