# Peptide membrane simulation **URL:** \ **Category:** User discussions\ **Created:** [October 29, 2025, 5:57am UTC](https://gromacs.bioexcel.eu/t/peptide-membrane-simulation/12848 "2025-10-29T05:57:55Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![rashiprasad](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/rashiprasad/32/4741_2.png) [@rashiprasad](https://gromacs.bioexcel.eu/u/rashiprasad)\ **Post date:** [October 29, 2025, 5:57am UTC](https://gromacs.bioexcel.eu/t/peptide-membrane-simulation/12848/1 "2025-10-29T05:57:56Z")
GROMACS version: 2024 GROMACS modification: Yes/No Here post your question Hi, So my query is that I have finished my simulation for my peptide membrane system, here my peptide is an AMP, and my membrane is an saureus bacterial membrane (POPE, POPG and TOCL1), I ran the simulation for 100ns. How to go about visualization, I corrected my trajectory and centered but later realised that it must have centered my peptide to the centre of the membrane as well, also, I had placed my peptide above water and my simulation was to see if the peptide gradually goes inside the membrane or ruptures for its antimicrobial properties, can someone please help me with analysis, maybe correcting the traj is making me visualize an artifact instead of real data. ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [October 29, 2025, 4:33pm UTC](https://gromacs.bioexcel.eu/t/peptide-membrane-simulation/12848/2 "2025-10-29T16:33:03Z")
Hi @rashiprasad The best thing that you can do is center the membrane in the box so that is staying still and see what happens, something like ```bash gmx trjconv -f your_traj.xtc -s your_tpr.tpr -pbc mol -center -o output.xtc ``` and select the membrane as centering group, outputting everything (or at least AMP + lipids). To see also where your ligand is you can check the distance between the center of mass of AMP and that of the bilayer along the z axis. ---
**Author:** ![rashiprasad](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/rashiprasad/32/4741_2.png) [@rashiprasad](https://gromacs.bioexcel.eu/u/rashiprasad)\ **Post date:** [October 31, 2025, 6:54am UTC](https://gromacs.bioexcel.eu/t/peptide-membrane-simulation/12848/3 "2025-10-31T06:54:59Z")
Hi @obZehn Thank you so much for the valuable input! ---
**Author:** ![MiSSSD](https://avatars.discourse-cdn.com/v4/letter/m/eb8c5e/32.png) [@MiSSSD](https://gromacs.bioexcel.eu/u/MiSSSD)\ **Post date:** [March 3, 2026, 3:01pm UTC](https://gromacs.bioexcel.eu/t/peptide-membrane-simulation/12848/4 "2026-03-03T15:01:23Z")
@rashiprasad Hi everyone So i had a question I generated a membrane from charmm gui, and put it for 100ns simulation, to equilibriate… Now i want to position my Peptide near the equilibriated Membrane ~2nm from the polar head… Can you guide me as to how to do it? I looked around and realized charmm-gui cannot work with pre-equilibriated membrane system. Thanks for your time. ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [March 3, 2026, 5:14pm UTC](https://gromacs.bioexcel.eu/t/peptide-membrane-simulation/12848/5 "2026-03-03T17:14:52Z")
Take a look at [gmx insert-molecules](https://manual.gromacs.org/current/onlinehelp/gmx-insert-molecules.html)! ---
**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:** [March 3, 2026, 8:24pm UTC](https://gromacs.bioexcel.eu/t/peptide-membrane-simulation/12848/6 "2026-03-03T20:24:51Z")
Just a note i wanted to add here that, It is unlikely that a rupture or insertion event occur from a 100 ns. ---
**Author:** ![MiSSSD](https://avatars.discourse-cdn.com/v4/letter/m/eb8c5e/32.png) [@MiSSSD](https://gromacs.bioexcel.eu/u/MiSSSD)\ **Post date:** [March 4, 2026, 4:12am UTC](https://gromacs.bioexcel.eu/t/peptide-membrane-simulation/12848/7 "2026-03-04T04:12:43Z")
will try and get back thanks a lot ---
**Author:** ![MiSSSD](https://avatars.discourse-cdn.com/v4/letter/m/eb8c5e/32.png) [@MiSSSD](https://gromacs.bioexcel.eu/u/MiSSSD)\ **Post date:** [March 13, 2026, 8:30am UTC](https://gromacs.bioexcel.eu/t/peptide-membrane-simulation/12848/8 "2026-03-13T08:30:54Z")
I ended up using the ppm orientation, and built the membrane peptide system using charmm-gui itself…but allowed for longer equilibration times. Sry guys!