GROMACS version: 2020.7
GROMACS modification: No
Hi,
I want to embed a protein in an equilibrated membrane model. I cannot use CHARMM-GUI for this purpose, as I need the membrane to be completely equilibrated before embedding the protein inside.
One option is to use gmx mdrun -membed from older versions of GROMACS. But I cannot find any tutorial or manual about this process. I would appreciate it if you could help me find a manual or explain how to use this method. I am not even sure how exactly one can derive .dat file that is needed. Alternatively, I would appreciate it if there is another method for embedding the protein inside a membrane that might be in the newer versions of GROMACS.
Bests,
Maryam