[gmx-users] System equilibration and interaction energy

aloks at mbu.iisc.ernet.in aloks at mbu.iisc.ernet.in
Tue Apr 25 10:54:05 CEST 2006

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

   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.
  if i look the potential energy of the system then from the begining
itself it seems to be equilibrated with a fluctuation of ~700kj/mol. I
guess that may be because of very high contribution from the solvent.

   For nearly 26000 atoms i have done the simulation upto 4 ns. So i would
just like to know that what is the best way to define system
equilibration when a major part is restrained.

2. my second question is about caluclation of the interaction energy
betwen the protein and the ligand. one possible way seems to be calculate
all the energy pairs given by gromacs with ligand and protein (ljsr, ljlr,
lj14 and for coulombs) and sum it or do i need to do two more simulations,
one with protein alone in the same box size with same number of water
molecules and other with the ligand alone and then substracting the sum of
potential energies of independent simulations from the protein-ligand

any suggestion would be highly appreciated


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