GROMACS version: 2018
GROMACS modification: No
I want to perform ion channel MD simulations using gromacs.
My objective is to study the inhibition of permeation of K+ ion through the channel by the ligand.
The tetramer of Kcsa protein is created using vmd (pdb id - 1k4c) with K+ ions in the channel. the water molecules are removed from the cavity
The ligand under study is docked using autodock. The Complex ( Protein+Ligand+Kions) is placed in the popc bilayer using charmm-gui.
Is there anything important to consider for this simulation?