# Uploading .gro file in VMD

**URL:** <https://gromacs.bioexcel.eu/t/uploading-gro-file-in-vmd/8046>\
**Category:** User discussions\
**Created:** [January 16, 2024, 10:58am UTC](https://gromacs.bioexcel.eu/t/uploading-gro-file-in-vmd/8046 "2024-01-16T10:58:31Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Rochik](https://avatars.discourse-cdn.com/v4/letter/r/ecc23a/32.png) [@Rochik](https://gromacs.bioexcel.eu/u/Rochik)\
**Post date:** [January 16, 2024, 10:58am UTC](https://gromacs.bioexcel.eu/t/uploading-gro-file-in-vmd/8046/1 "2024-01-16T10:58:31Z")

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GROMACS version: 2023

Dear all,  
I have a very simple question. I want to open my trajectory file (md.xtc) using VMD, and I need to upload the necessary .gro file first. Here’s my question:  
Which .gro file should be uploaded? the .gro file of the starting point of the production phase or the last point?  
I also have another question. Is npt.gro exactly the starting point of the production phase?  
Thank you so much

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**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\
**Post date:** [January 17, 2024, 2:07pm UTC](https://gromacs.bioexcel.eu/t/uploading-gro-file-in-vmd/8046/2 "2024-01-17T14:07:25Z")

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The .xtc file does not contain atom/residue names, so these are taken from the structure file (.gro or .pdb). In that regard, it doesn’t really matter which one you use, and you can remove the respective frame within VMD if you don’t want it to add to the trajectory; for example, if you do

```auto
vmd traj.xtc struct.gro

```

the command will work but the (potentially initial) .gro file will be added at the end of the trajectory, and it can mess up some time-series analyses.

Regarding the second question, it’s hard to answer exactly unless you share your full workflow, as there are no universal naming conventions for Gromacs. But if you run a job with e.g. `-deffnm npt`, then `npt.gro` will contain the last frame from that simulation part.

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**Author:** ![Rochik](https://avatars.discourse-cdn.com/v4/letter/r/ecc23a/32.png) [@Rochik](https://gromacs.bioexcel.eu/u/Rochik)\
**Post date:** [January 17, 2024, 2:15pm UTC](https://gromacs.bioexcel.eu/t/uploading-gro-file-in-vmd/8046/3 "2024-01-17T14:15:13Z")

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Thank you so much for your useful information

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**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\
**Post date:** [January 17, 2024, 9:26pm UTC](https://gromacs.bioexcel.eu/t/uploading-gro-file-in-vmd/8046/4 "2024-01-17T21:26:04Z")

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You can extract the first frame of the trajectory and load that first then trajectory. @Rochik

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**Author:** ![Rochik](https://avatars.discourse-cdn.com/v4/letter/r/ecc23a/32.png) [@Rochik](https://gromacs.bioexcel.eu/u/Rochik)\
**Post date:** [January 18, 2024, 10:00am UTC](https://gromacs.bioexcel.eu/t/uploading-gro-file-in-vmd/8046/5 "2024-01-18T10:00:01Z")

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Thank you @scinikhil. That sounds a good idea!