[gmx-users] metal ions in equilibration step

[Mahboobeh Eslami]

Hi all GMX usersI want to do MD simulation on protein-ligand complex. There are two calcium ions in the protein structure. These ions play an important role. In the equilibration step,  should I consider protein,ligand and calcium ions as one single entity (for tc_grps option)? or should I consider these calcium as the part of ions in sol-ions group?ThanksBest