# Protein ligand tutorial gone wrong? Maybe? VMD

**URL:** <https://gromacs.bioexcel.eu/t/protein-ligand-tutorial-gone-wrong-maybe-vmd/6480>\
**Category:** User discussions\
**Tags:** mdrun, analysis-tools, simulation-setup\
**Created:** [May 24, 2023, 6:44am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-tutorial-gone-wrong-maybe-vmd/6480 "2023-05-24T06:44:32Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Noob](https://avatars.discourse-cdn.com/v4/letter/n/5e9695/32.png) [@Noob](https://gromacs.bioexcel.eu/u/Noob)\
**Post date:** [May 24, 2023, 6:44am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-tutorial-gone-wrong-maybe-vmd/6480/1 "2023-05-24T06:44:32Z")

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GROMACS version: 2023  
GROMACS modification: No  
Here post your question  
I’m not sure if this has more to do with VMD or GROMACS or I messed up on both, but here we go.  
So I was following the Protein-Ligand tutorial for gromacs, and got all the way to the Production of MD stage and got my `md_0_10.gro` and `md_0_10.xtc` files then I thought to visualize them in VMD. And this is were my question comes from. So when I first loaded up the files and got a visual repsentation at first it seem normal:

 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/a/a45459899612afd13163df0cf33850d907615fda.png)

But then as more and more frames pasted it start to look like it’s glitching:

 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/a/ab5cd8637bbbe7488006beb05b46ba8c61a75612.png)

I thought this may be a problem with the ribbon drawing method but I get the same porblem with the lines drawing method and it seems more appearent

 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/9/9fd456e35fae5d569a3f8d3f6851a95d51ddbddf.png)

And my question is did I do something wrong?

If so what? Is it a problem with the ‘topol.top’ file? If not what?

If not, then what I’m I looking at? Or why does it do this? Do protein under a mircoscope glitch out like this too? What exactly is this image/video suppose to model?

And just too add on, you prbably noticed I turned off the water representation, but when I turn it back on it has the exact same line stuff going on:

 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/3/32a5181b828668620fb999ae2dbf00d11b55f2fc.jpeg)

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<div class="post-metadata">

**Author:** ![Noob](https://avatars.discourse-cdn.com/v4/letter/n/5e9695/32.png) [@Noob](https://gromacs.bioexcel.eu/u/Noob)\
**Post date:** [May 24, 2023, 3:31pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-tutorial-gone-wrong-maybe-vmd/6480/2 "2023-05-24T15:31:30Z")

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Nevermind I’m an idiot