# Non-Prebound Protein and Membrane Bonding simulation

**URL:** <https://gromacs.bioexcel.eu/t/non-prebound-protein-and-membrane-bonding-simulation/2510>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [July 14, 2021, 6:01pm UTC](https://gromacs.bioexcel.eu/t/non-prebound-protein-and-membrane-bonding-simulation/2510 "2021-07-14T18:01:27Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![gpoetker](https://avatars.discourse-cdn.com/v4/letter/g/cc9497/32.png) [@gpoetker](https://gromacs.bioexcel.eu/u/gpoetker)\
**Post date:** [July 14, 2021, 6:01pm UTC](https://gromacs.bioexcel.eu/t/non-prebound-protein-and-membrane-bonding-simulation/2510/1 "2021-07-14T18:01:27Z")

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GROMACS version: 2020.5  
GROMACS modification: No  
Here post your question

I am currently trying to run a md simulation of a protein binding to a membrane and I can’t find where to start. I currently have these input files  
(and other CHARMM-Gui outputs for membrane only development)  
Protein.pdb  
Membrane.pdb  
MembraneIndex.ndx  
Membrane.gro  
MembraneTopol.top  
Lipid1.itp  
Lipid2.itp

What do i need to do to simulate this interaction? am i on the right track? Thank you!

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**Author:** ![JakubH](https://avatars.discourse-cdn.com/v4/letter/j/df788c/32.png) [@JakubH](https://gromacs.bioexcel.eu/u/JakubH)\
**Post date:** [July 16, 2021, 11:57am UTC](https://gromacs.bioexcel.eu/t/non-prebound-protein-and-membrane-bonding-simulation/2510/2 "2021-07-16T11:57:37Z")

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I never do protein binding to a membrane, because I simulate mostly only membrane system (without proteins, but I think you should check the tutorials [GROMACS Tutorials](http://www.mdtutorials.com/gmx/)

You should try to do **[Tutorial 2: KALP15 in DPPC](http://www.mdtutorials.com/gmx/membrane_protein/index.html)** because this is a system with membrane and protein. First you should build the system, then (I see that you build your system in charmm-gui) then minimize energy, equilibrate and run md simulation like in the tutorial and then analyze some parameters.