# Protein-ligand-membrane simulation **URL:** \ **Category:** User discussions\ **Created:** [August 31, 2025, 7:16am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-membrane-simulation/12589 "2025-08-31T07:16:56Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![AF1](https://avatars.discourse-cdn.com/v4/letter/a/eada6e/32.png) [@AF1](https://gromacs.bioexcel.eu/u/AF1)\ **Post date:** [August 31, 2025, 7:16am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-membrane-simulation/12589/1 "2025-08-31T07:16:56Z")
GROMACS version: 2024 Hello, is there any tutorial for simulating a protein-ligand-membrane system? I am familiar with simulating protein and protein-ligand. I know how to build a membrane system on CHARMM-GUI but never proceeded with the actual simulation. Should I prepare the membrane system using the protein-ligand complex pdb file? and for the simulation kindly let me know if there is any tutorial? Thanks. ---
**Author:** ![danielgruiz](https://avatars.discourse-cdn.com/v4/letter/d/db5fbb/32.png) [@danielgruiz](https://gromacs.bioexcel.eu/u/danielgruiz)\ **Post date:** [September 5, 2025, 11:35am UTC](https://gromacs.bioexcel.eu/t/protein-ligand-membrane-simulation/12589/2 "2025-09-05T11:35:29Z")
Hi, I do not have a lot of experience but currently I am performing a MD simulation with membrane receptor and ligands. Particulary, I prefered to prepare the membrane receptor entity with CHARMMGUI and develop the NVT equilibration step with CHARMMGUI too. After get the pre-nvt system in .pdb and the steps nvt.mdp configurations with constrains created (.itp files) by CHARMMGUI, I started to generate the pre-nvt system .gro file without waters using gmx pdb2gmx. In sequence, I applied the tutorial of Ligand-protein complex and the membrane protein tutorial, at this final tutorial only consider the steps after the membrane building. When I arrives in minimization steps in both equilibrations I used the information of the em.mdp, nvt.mdp and .itp generated by CHARMMGUI to adpt the simulation. ---
**Author:** ![AF1](https://avatars.discourse-cdn.com/v4/letter/a/eada6e/32.png) [@AF1](https://gromacs.bioexcel.eu/u/AF1)\ **Post date:** [September 5, 2025, 12:39pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-membrane-simulation/12589/3 "2025-09-05T12:39:21Z")
Hello Thank you for the response. It is however still not that clear. Would you mind sharing an email that I can contact you? ---
**Author:** ![danielgruiz](https://avatars.discourse-cdn.com/v4/letter/d/db5fbb/32.png) [@danielgruiz](https://gromacs.bioexcel.eu/u/danielgruiz)\ **Post date:** [September 13, 2025, 3:24pm UTC](https://gromacs.bioexcel.eu/t/protein-ligand-membrane-simulation/12589/4 "2025-09-13T15:24:00Z")
Yes, you can. my e-mail: daniel.g.ruiz@unesp.br