From f45409a18fe0cb2a3515284a9b2b1db72c3b71a3 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Mon, 26 Feb 2018 09:43:55 +0100
Subject: [PATCH] Added warning about whole molecules
---
src/colvar/Dipole.cpp | 5 +++++
src/colvar/PathMSD.cpp | 4 ++++
src/colvar/PropertyMap.cpp | 4 ++++
src/colvar/RMSD.cpp | 4 ++++
4 files changed, 17 insertions(+)
diff --git a/src/colvar/Dipole.cpp b/src/colvar/Dipole.cpp
index 5f6748db6..170221ac4 100644
--- a/src/colvar/Dipole.cpp
+++ b/src/colvar/Dipole.cpp
@@ -34,6 +34,11 @@ namespace colvar {
/*
Calculate the dipole moment for a group of atoms.
+\warning
+The atoms used for \ref DIPOLE calculation should be from a whole molecule.
+In case the molecule is broken by the host MD code, please use \ref WHOLEMOLECULES to reconstruct it before \ref DIPOLE calculation.
+
+
\par Examples
The following tells plumed to calculate the dipole of the group of atoms containing
diff --git a/src/colvar/PathMSD.cpp b/src/colvar/PathMSD.cpp
index 86fb1deda..f1031a7d0 100644
--- a/src/colvar/PathMSD.cpp
+++ b/src/colvar/PathMSD.cpp
@@ -37,6 +37,10 @@ This variable computes the progress along a given set of frames that is provided
in input ("sss" component) and the distance from them ("zzz" component).
(see below).
+\warning
+The molecule used for \ref PATHMSD calculation should be whole (both atoms used in alignment and in displacement calculation).
+In case it is broken by the host MD code, please use \ref WHOLEMOLECULES to reconstruct it before \ref PATHMSD calculation.
+
\par Examples
Here below is a case where you have defined three frames and you want to
diff --git a/src/colvar/PropertyMap.cpp b/src/colvar/PropertyMap.cpp
index cee9c313e..9c6ef5198 100644
--- a/src/colvar/PropertyMap.cpp
+++ b/src/colvar/PropertyMap.cpp
@@ -45,6 +45,10 @@ zzz=-\frac{1}{\lambda}\log(\sum_i \exp(-\lambda D_i(x)))
where the parameters \f$X_i\f$ and \f$Y_i\f$ are provided in the input pdb (allv.pdb in this case) and
\f$D_i(x)\f$ is the MSD after optimal alignment calculated on the pdb frames you input (see Kearsley).
+\warning
+The molecule used for \ref PROPERTYMAP calculation should be whole (both atoms used in alignment and in displacement calculation).
+In case it is broken by the host MD code, please use \ref WHOLEMOLECULES to reconstruct it before \ref PROPERTYMAP calculation.
+
\par Examples
\verbatim
diff --git a/src/colvar/RMSD.cpp b/src/colvar/RMSD.cpp
index bdc9b4ac5..946e409c9 100644
--- a/src/colvar/RMSD.cpp
+++ b/src/colvar/RMSD.cpp
@@ -128,6 +128,10 @@ all the atoms in the segment are assumed to be part of both the alignment and di
Please note that there are a number of other methods for calculating the distance between the instantaneous configuration and a reference configuration
that are available in plumed. More information on these various methods can be found in the section of the manual on \ref dists.
+\warning
+The molecule used for \ref RMSD calculation should be whole (both atoms used in alignment and in displacement calculation).
+In case it is broken by the host MD code, please use \ref WHOLEMOLECULES to reconstruct it before \ref RMSD calculation.
+
\par Examples
The following tells plumed to calculate the RMSD distance between
--
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