Questions and problems?

'Belly' options with AMBER

While running an equilibration of protein in water, I allow only the water molecules to move using the belly option. However the protein moves during the simulation, ie there is a non zero rmsd with the starting structure. It seems that the protein is being compressed. I obtained similar results when constraining the protein using a harmonic potential.

With constant pressure applied, the restrained coordinates or those held fixed with the belly option are not truly fixed, since the coordinates are still scaled up and down as the box size changes to maintain constant pressure. Moreover, since the box has a corner at the origin, this scaling moves atoms (or with NPSCAL=1, molecules) to and from this corner of the box. This is normally only noticable during volume equilibration with constant pressure, since the box is monotonically shrinking. See the discussion of equilibration for more on this.

In the end, the apparent deviation from your starting structure doesn't matter: a little minimization will make things as chemically right as before, whatever scaling options are used, and more to the point you are preparing to run without belly with gradual warming (or gradual relaxation of harmonic restraints) as part of the equilibration, and this means you a) don't even need to minimize since dynamics will have the same effect b) you are about to abandon your initial coordinates anyway.