Peptide membrane simulation

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GROMACS version: 2024
GROMACS modification: Yes/No
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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.

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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

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.

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Hi @obZehn Thank you so much for the valuable input!