diff --git a/src/generic/MolInfo.cpp b/src/generic/MolInfo.cpp index d68aaee9ea..f56b143aae 100644 --- a/src/generic/MolInfo.cpp +++ b/src/generic/MolInfo.cpp @@ -49,11 +49,11 @@ generated with `gmx editconf -f topol.tpr -o reference.pdb`. More information of the PDB parser implemented in PLUMED can be found \ref pdbreader "at this page". If the flag `WHOLE` is used, the reference structure is assumed to be whole, i.e. not broken by PBC. -**This will impact PDB calculations in all the actions following the MOLINFO action!**. +**This will impact PBC calculations in all the actions following the MOLINFO action!**. In particular, actions that reconstruct molecules locally will do the reconstruction using a minimum spanning tree rather than the order in which atoms are provided. -Notice that PLUMED 2.8 and 2.9 this would only have affected the behavior of \ref WHOLEMOLECULES -actions, whereas starting with PLUMED 2.10 all actions that reconstruct PBCs are affected. +Notice that in PLUMED 2.8, 2.9, and 2.10 this would only have affected the behavior of \ref WHOLEMOLECULES +actions, whereas starting with PLUMED 2.11 all actions that reconstruct PBCs are affected. If you want a variable to ignore this, you can just repeate the MOLINFO action without the `WHOLE` flag: all the following actions will use the traditional reconstruction algorithm, based on the order in which atoms are listed. diff --git a/src/generic/WholeMolecules.cpp b/src/generic/WholeMolecules.cpp index e883099cf8..7dc244f6a0 100644 --- a/src/generic/WholeMolecules.cpp +++ b/src/generic/WholeMolecules.cpp @@ -137,7 +137,7 @@ void WholeMolecules::registerKeywords( Keywords& keys ) { "specifying all. Alternatively, if you wish to use a subset of the residues you can specify the particular residues " "you are interested in as a list of numbers"); keys.add("optional","MOLTYPE","the type of molecule that is under study. This is used to define the backbone atoms"); - keys.addFlag("EMST", false, "only for backward compatibility, as of PLUMED 2.10 this is the default when using MOLINFO with WHOLE"); + keys.addFlag("EMST", false, "only for backward compatibility, as of PLUMED 2.11 this is the default when using MOLINFO with WHOLE"); keys.addFlag("ADDREFERENCE", false, "Define the reference position of the first atom of each entity using a PDB file"); } @@ -151,7 +151,7 @@ WholeMolecules::WholeMolecules(const ActionOptions&ao): // parse optional flags bool doemst_tmp; parseFlag("EMST", doemst_tmp); - if(doemst_tmp) log << "EMST option is not needed any more as of PLUMED 2.10\n"; + if(doemst_tmp) log << "EMST option is not needed any more as of PLUMED 2.11\n"; parseFlag("ADDREFERENCE", addref); auto* moldat=plumed.getActionSet().selectLatest(this);