# Possible artefacts during trajectory unwrapping using -pbc nojump

**URL:** <https://gromacs.bioexcel.eu/t/possible-artefacts-during-trajectory-unwrapping-using-pbc-nojump/12005>\
**Category:** User discussions\
**Created:** [April 29, 2025, 2:38pm UTC](https://gromacs.bioexcel.eu/t/possible-artefacts-during-trajectory-unwrapping-using-pbc-nojump/12005 "2025-04-29T14:38:06Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![abelxf](https://avatars.discourse-cdn.com/v4/letter/a/cdc98d/32.png) [@abelxf](https://gromacs.bioexcel.eu/u/abelxf)\
**Post date:** [April 29, 2025, 2:38pm UTC](https://gromacs.bioexcel.eu/t/possible-artefacts-during-trajectory-unwrapping-using-pbc-nojump/12005/1 "2025-04-29T14:38:06Z")

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GROMACS version:2021  
GROMACS modification: No

I am attempting to calculate the lateral diffusion of lipid species from MARTINI2.2 simulations implemented using GROMACS. I followed the following steps for pbc corrections and unwrapping.  
Step 1 :- -pbc mol -center ; System for centering and output  
Step 2 :- -pbc atom -center ; Membrane for centering and output  
Step 3 :- -pbc whole ; Membrane as output  
Step 4 :- -pbc nojump ; Membrane output

While calculating the MSD, I observed a significantly non-linear rise in the MSD towards the last 1 microsecond of the simulation. Funnily enough, I observed this for both a trajectory that is 5us long and 10us long! The blow up was only at the last 1us in both cases. Has anyone else encountered such an issue before? I suspect this is some artefact of trajectory unwrapping.  
P.S: I used both lipyphilic as well as code that I had written myself to calculate the MSD and got the same results.