[gmx-users] System equilibration and interaction energy

[aloks at mbu.iisc.ernet.in]

Dear Gromacs users,

I have two queries :
1. I am doing simulation for a protein (156 residues ) with a sugar. Out
of 156 protein resiudes i have restrained 130 residues and rest part  i
have kept free. My doubt is that when we can say that system has
equilibrated?

if on the basis of rmsd then i dont feel it would be advisable to look the
rmsd of protein because major part i have restrained, if i consider  sugar
rmsd then i can see a kind of periodicity in the rmsd. if i look the rmsd
of the system then it seems to be stablized at 4.5nm.