# Analysis and trajectory conversion

**URL:** <https://gromacs.bioexcel.eu/t/analysis-and-trajectory-conversion/403>\
**Category:** User discussions\
**Created:** [June 30, 2020, 12:25pm UTC](https://gromacs.bioexcel.eu/t/analysis-and-trajectory-conversion/403 "2020-06-30T12:25:16Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![azadeh](https://avatars.discourse-cdn.com/v4/letter/a/cab0a1/32.png) [@azadeh](https://gromacs.bioexcel.eu/u/azadeh)\
**Post date:** [June 30, 2020, 12:25pm UTC](https://gromacs.bioexcel.eu/t/analysis-and-trajectory-conversion/403/1 "2020-06-30T12:25:16Z")

</div>

GROMACS version: 2018  
GROMACS modification: No

Dear all

I have simulated a membrane system using PBC and without giving any command for the removal of the center of mass in the mdp file. I would like to know generally for the analysis of this system, specifically the RDF and MSD analysis tools of GROMACS, should I use trjconv to convert the trajectory, and if so, which steps should I go through.

Thank you very much for your help.

Best,  
Azadeh

---

<div class="post-metadata">

**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:** [July 2, 2020, 8:24pm UTC](https://gromacs.bioexcel.eu/t/analysis-and-trajectory-conversion/403/2 "2020-07-02T20:24:17Z")

</div>

Typically, gromacs does necessary trajectory conversion (e.g. -pbc whole/nojump), users do not need to do explicitly. There are few notes,

- For COM based RDF, you need to have whole molecules. You can convert trajectory with -pbc whole, then do RDF. Check if you get similar answer without conversion.

- For MSD calculation, The whole molecules should be unwrapped, Which can be achieved,

Gromacs does this automatically, yet I would do it manually and check against unconverted trajectory.

- Even though, you didn’t specify comm-mode/nstcomm, gromacs by default removes after every 100 steps. COM removal is necessary for MSD, otherwise you would get higher self-diffusion due to global motion arises from accumulation of kinetic energy.

Thanks  
Masrul