Variable-cell calculations (both optimization and dynamics) are performed with plane waves and G-vectors calculated for the starting cell. Only the last step, after convergence has been achieved, is performed for the converged structure, with plane waves and G-vectors calculated for the final cell. Small differences between the two last steps are thus to be expected and give an estimate of the convergence of the variable-cell optimization with respect to the plane-wave basis. A large difference means that you are far from convergence in the plane-wave basis set and you need to increase the cutoff(s) ecutwfc and/or (if applicable) ecutrho.
"A common mistake many new users make is to set the time step dt improperly to the same order of magnitude as for CP algorithm, or not setting dt at all. This will produce a ``not evolving dynamics''. Good values for the original RMW (Wentzcovitch) dynamics are dt = 50÷70. The choice of the cell mass is a delicate matter. An off-optimal mass will make convergence slower. Too small masses, as well as too long time steps, can make the algorithm unstable. A good cell mass will make the oscillation times for internal degrees of freedom comparable to cell degrees of freedom in non-damped Variable-Cell MD. Test calculations are advisable before extensive calculation. I have tested the damping algorithm that I have developed and it has worked well so far. It allows for a much longer time step (dt= 100÷150) than the RMW one and is much more stable with very small cell masses, which is useful when the cell shape, not the internal degrees of freedom, is far out of equilibrium. It also converges in a smaller number of steps than RMW." (Info from Cesar Da Silva: the new damping algorithm is the default since v. 3.1).