Peptide penetration into lipid bilayer simulation using Martini and umbrella sampling

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1

GROMACS version:2024
GROMACS modification: No

Can someone suggest some tutorials for simulating peptide penetration into lipid bilayer using MARTINI and the umbrella sampling method?

I have tried to generate the initial structure of CG lipid and peptide using CHARMM-GUI and equilibrated the system. The pull .mdp file for umbrella sampling from Umbrella Sampling.
as the tutorial is for all-atom protein simulation. The pressure coupling, temperature coupling, and various other parameter values are different.

Please let me know, If there is any tutorial for the same or provide me with a sample .mdp file.

thanks!
Rakesh

2

Dear @rakeshk

The important part of the sampling tutorial is the part where you define the groups and the pulling, that is, where you set pull = yes and some of the following parameters. If you have already run em/NVT/NpT simulations to equilibrate the systems then you have already all the parameters you need to run a pull simulation (to generate the starting configurations) and the corresponding sampling runs. These parameters will be most likely already reported in the sample .mdp files from CHARMM-GUI.

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