# How to get the wnrapped trajectory file?

**URL:** <https://gromacs.bioexcel.eu/t/how-to-get-the-wnrapped-trajectory-file/10306>\
**Category:** User discussions\
**Created:** [October 9, 2024, 11:11am UTC](https://gromacs.bioexcel.eu/t/how-to-get-the-wnrapped-trajectory-file/10306 "2024-10-09T11:11:53Z")\
**Posts on this page:** 9\
**Page:** 1

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**Author:** ![mj.rezayani](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mj.rezayani/32/3918_2.png) [@mj.rezayani](https://gromacs.bioexcel.eu/u/mj.rezayani)\
**Post date:** [October 9, 2024, 11:11am UTC](https://gromacs.bioexcel.eu/t/how-to-get-the-wnrapped-trajectory-file/10306/1 "2024-10-09T11:11:53Z")

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Dear Gromacs users:

I want to write a code to calculate MSD using Gromacs trajectory. I changed the trajectory file to the text file using gmx dump. However, I figured out the trajectory is in the wrapped form which does not show the real trajectory of the diffusant outside of the box. I need the real distance traversed by the atoms.

What should I do to get the unwrapped trajectory file?

Thanks

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [October 9, 2024, 2:15pm UTC](https://gromacs.bioexcel.eu/t/how-to-get-the-wnrapped-trajectory-file/10306/2 "2024-10-09T14:15:40Z")

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Do you mean `gmx trjconv -pbc nojump`?

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**Author:** ![mj.rezayani](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mj.rezayani/32/3918_2.png) [@mj.rezayani](https://gromacs.bioexcel.eu/u/mj.rezayani)\
**Post date:** [October 9, 2024, 3:27pm UTC](https://gromacs.bioexcel.eu/t/how-to-get-the-wnrapped-trajectory-file/10306/3 "2024-10-09T15:27:53Z")

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Thanks for your reply,

but it just shows the movement in just positive direction. I mean the molecules cross the box from just 3 dimensions of the cube. (x,y and z) instead of (x,y,z,-x,-y,-z)

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [October 9, 2024, 3:34pm UTC](https://gromacs.bioexcel.eu/t/how-to-get-the-wnrapped-trajectory-file/10306/4 "2024-10-09T15:34:34Z")

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I don’t understand what you mean.

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**Author:** ![mj.rezayani](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mj.rezayani/32/3918_2.png) [@mj.rezayani](https://gromacs.bioexcel.eu/u/mj.rezayani)\
**Post date:** [October 14, 2024, 10:58am UTC](https://gromacs.bioexcel.eu/t/how-to-get-the-wnrapped-trajectory-file/10306/5 "2024-10-14T10:58:12Z")

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Dear MagnusL,

Sorry for the late response. As you can see the water molecules are going out of the box in 3 directions. Indeed, we expect for 6 directions. The pink structure is Zeolite and blue is water.

Thanks

 ![Screenshot from 2024-10-14 12-54-21](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/6/699ce2a327b7b7c3214e02c22d39600b95a8bdb0.jpeg)

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [October 15, 2024, 6:19am UTC](https://gromacs.bioexcel.eu/t/how-to-get-the-wnrapped-trajectory-file/10306/6 "2024-10-15T06:19:24Z")

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That looks strange indeed. Would you be able to share the xtc file somewhere, and preferably also confout.gro from the simulation?

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**Author:** ![mj.rezayani](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mj.rezayani/32/3918_2.png) [@mj.rezayani](https://gromacs.bioexcel.eu/u/mj.rezayani)\
**Post date:** [October 15, 2024, 10:01am UTC](https://gromacs.bioexcel.eu/t/how-to-get-the-wnrapped-trajectory-file/10306/7 "2024-10-15T10:01:39Z")

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Thanks for your reply.

I don’t know how I can share my .xtc file. Do you have any suggestions?

Thanks

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<div class="post-metadata">

**Author:** ![mj.rezayani](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mj.rezayani/32/3918_2.png) [@mj.rezayani](https://gromacs.bioexcel.eu/u/mj.rezayani)\
**Post date:** [October 15, 2024, 10:09am UTC](https://gromacs.bioexcel.eu/t/how-to-get-the-wnrapped-trajectory-file/10306/8 "2024-10-15T10:09:53Z")

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Dear MagnusL

I found the main problem.` -pbc nojump` is working correctly.

Thanks a lot.

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [October 15, 2024, 12:32pm UTC](https://gromacs.bioexcel.eu/t/how-to-get-the-wnrapped-trajectory-file/10306/9 "2024-10-15T12:32:40Z")

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Great to hear!