Bug List
Page amber14
Charges passed from amber to plumed are in wrong units and thus lead to wrong results for variables depending on their values. See http://github.com/plumed/plumed2/issues/165 for more details.
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 HISTOGRAM
Option FREE-ENERGY or UNNORMALIZED without USE_ALL_DATA is not working properly. See #175.
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-2.8
NAMD does not currently take into account virial contributions from PLUMED. Please use constant volume simulations only
Page namd-2.9
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.