Bug List
Page CENTER_OF_MULTICOLVAR
The virial contribution for this type of virtual atom is not currently evaluated so do not use in bias functions unless the volume of the cell is fixed
Page ENERGY
Acceptance for replica exchange when ENERGY is biased is computed correctly only of all the replicas has the same potential energy function. This is for instance not true when using GROMACS with lambda replica exchange of with plumed-hrex branch.
Page lammps-6Apr13
The provided patch does not pass the virial correctly to PLUMED (see https://github.com/plumed/plumed2/issues/377). If you need to perform constant pressure simulations you should download a LAMMPS version newer than November 2018, where the mentioned bug has been fixed, that natively supports PLUMED 2.4.
Page MOLINFO

At the moment the HA1 atoms in a GLY residues are treated as if they are the CB atoms. This may or may not be true - GLY is problematic for secondary structure residues as it is achiral.

If you use WHOLEMOLECULES RESIDUES=1-10 for a 18 amino acid protein ( 18 amino acids + 2 terminal groups = 20 residues ) the code will fail as it will not be able to interpret terminal residue 1.

Page namd-2.12
NAMD does not currently take into account virial contributions from PLUMED. Please use constant volume simulations only.
Page namd-2.13
NAMD does not currently take into account virial contributions from PLUMED. Please use constant volume simulations only.
Page PCAVARS
It is not possible to use the DRMSD metric with this variable. You can get around this by listing the set of distances you wish to calculate for your DRMSD in the plumed file explicitally and using the EUCLIDEAN metric. MAHALONOBIS and NORM-EUCLIDEAN also do not work with this variable but using these options makes little sense when projecting on a linear subspace.
Page PUCKERING
The 6-membered ring implementation distributed with this version of PLUMED leads to qx and qy values that have an opposite sign with respect to those originally defined in [34]. The bug will be fixed in a later version but is here kept to preserve reproducibility.