GROMACS version:2023.1
GROMACS modification: Yes/No
Here post your question ：I wonder is there any protocal for antimcrobial peptide simulation on penetrating the membrane? I have used the CHARMM-GUI to built the lipid bilayer and simply put the peptide up the bilayer. But when I run the energy minimization, Fmax was much higher than 1000. Is there any suggestion to solve this problem?
There are almost certainly atoms overlapping. How did you “put the peptide up the bilayer”? You can use gmx insert-molecules. There are options to specify approximately where to insert it and, if you need to, you can scale down the inserted molecule to make it fit somewhere. But if you scale it down too much you will run into the same problem.
Thank you for your answer.
I have used gmx editconf to put the peptide totally up the membrane before, and I changed to gmx insert-molecules this time for insert the peptide up the upper leaflet. But this time, after EM, the peptide jumped to the downside of the lower leaflet. So, how can I remain the peptide up the upperleaflet after EM?
Try using restraints to keep it in place during EM and early equilibration stages.