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This ENERGY does not include long tail corrections. Thus when using e.g. LAMMPS "pair_modify tail yes" or GROMACS "DispCorr Ener" (or "DispCorr EnerPres"), the potential energy from ENERGY will be slightly different form the one of the MD code. You should still be able to use ENERGY and then reweight your simulation with the correct MD energy value.
Acceptance for replica exchange when ENERGY is biased is computed correctly only if all the replicas have the same potential energy function. This is for instance not true when using GROMACS with lambda replica exchange or with plumed-hrex branch.
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.
1.8.17