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.