# Visualization of membrane-embedded protein after MD simulations

**URL:** <https://gromacs.bioexcel.eu/t/visualization-of-membrane-embedded-protein-after-md-simulations/5087>\
**Category:** User discussions\
**Tags:** analysis-tools\
**Created:** [October 22, 2022, 11:15am UTC](https://gromacs.bioexcel.eu/t/visualization-of-membrane-embedded-protein-after-md-simulations/5087 "2022-10-22T11:15:35Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![cfr](https://avatars.discourse-cdn.com/v4/letter/c/90ced4/32.png) [@cfr](https://gromacs.bioexcel.eu/u/cfr)\
**Post date:** [October 22, 2022, 11:15am UTC](https://gromacs.bioexcel.eu/t/visualization-of-membrane-embedded-protein-after-md-simulations/5087/1 "2022-10-22T11:15:35Z")

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GROMACS version: 2020.6  
GROMACS modification: No

Hi,

I have run various simulations of a membrane-embedded protein in GROMACS. To aid my analysis, I would like to plot (via either Pymol or VMD) the configuration of the protein in a “sliced” membrane (like this figure: [https://lightdock.org/tutorials/0.9.1/membrane/3x29\_membrane.png](https://lightdock.org/tutorials/0.9.1/membrane/3x29_membrane.png) ).  
I could not find any easy way to do so; do you have any suggestions on how to do that?

Thank you