Once PWscf is patched with the PLUMED plug-in, it is possible to use most PLUMED functionalities by running PWscf as: ./pw.x -plumed plus the other usual PWscf arguments. The input file for PLUMED must be found in the specified outdir with fixed name plumed.dat.
Since v.4.2 the newer BFGS algorithm covers the case of variable-cell optimization as well. Note however that variable-cell calculations (both optimization and dynamics) are performed with plane waves and G-vectors calculated for the starting cell. This means that if you re-run a self-consistent calculation for the final cell and atomic positions using the same cutoff ecutwfc (and/or ecutrho if applicable), you may not find exactly the same results, unless your final and initial cells are very similar, or unless your cutoff(s) are very high. In order to provide a further check, a last step is performed in which a scf calculation 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 reliability of the variable-cell optimization. If you get a large difference, you are likely quite far from convergence in the plane-wave basis set and you need to increase the cutoff(s).
"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 (RM 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).