PROPERTYMAP
 This is part of the colvar module

Calculate generic property maps.

This Colvar calculates the property maps according to the work of Spiwok [107].

Basically it calculates

\begin{eqnarray*} X=\frac{\sum_i X_i*\exp(-\lambda D_i(x))}{\sum_i \exp(-\lambda D_i(x))} \\ Y=\frac{\sum_i Y_i*\exp(-\lambda D_i(x))}{\sum_i \exp(-\lambda D_i(x))} \\ \cdots\\ zzz=-\frac{1}{\lambda}\log(\sum_i \exp(-\lambda D_i(x))) \end{eqnarray*}

where the parameters $$X_i$$ and $$Y_i$$ are provided in the input pdb (allv.pdb in this case) and $$D_i(x)$$ is the mean squared displacement after optimal alignment calculated on the pdb frames you input (see Kearsley).

When running with periodic boundary conditions, the atoms should be in the proper periodic image. This is done automatically since PLUMED 2.5, by considering the ordered list of atoms and rebuilding molecules using a procedure that is equivalent to that done in WHOLEMOLECULES . Notice that rebuilding is local to this action. This is different from WHOLEMOLECULES which actually modifies the coordinates stored in PLUMED.

In case you want to recover the old behavior you should use the NOPBC flag. In that case you need to take care that atoms are in the correct periodic image.

Examples
Click on the labels of the actions for more information on what each action computes
p3: PROPERTYMAP REFERENCEcompulsory keyword
the pdb is needed to provide the various milestones =allv.pdb PROPERTYcompulsory keyword
the property to be used in the indexing: this goes in the REMARK field of the reference
=X,Y LAMBDAcompulsory keyword
the lambda parameter is needed for smoothing, is in the units of plumed =69087 NEIGH_SIZEsize of the neighbor list =8 NEIGH_STRIDEhow often the neighbor list needs to be calculated in time units =4
PRINT ARGthe input for this action is the scalar output from one or more other actions. =p3.X,p3.Y,p3.zzz STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output =1 FILEthe name of the file on which to output these quantities =colvar FMTthe format that should be used to output real numbers =%8.4f


note that NEIGH_STRIDE=4 NEIGH_SIZE=8 control the neighbor list parameter (optional but recommended for performance) and states that the neighbor list will be calculated every 4 steps and consider only the closest 8 member to the actual md snapshots.

In this case the input line instructs plumed to look for two properties X and Y with attached values in the REMARK line of the reference pdb (Note: No spaces from X and = and 1 !!!!). e.g.

REMARK X=1 Y=2
ATOM      1  CL  ALA     1      -3.171   0.295   2.045  1.00  1.00
ATOM      5  CLP ALA     1      -1.819  -0.143   1.679  1.00  1.00
END
REMARK X=2 Y=3
ATOM      1  CL  ALA     1      -3.175   0.365   2.024  1.00  1.00
ATOM      5  CLP ALA     1      -1.814  -0.106   1.685  1.00  1.00
END

Note
The implementation of this collective variable and of PATHMSD is shared, as well as most input options.
Glossary of keywords and components
Description of components

The names of the components in this action can be customized by the user in the actions input file. However, in addition to the components that can be customized the following quantities will always be output

 Quantity Description zzz the minimum distance from the reference points
Compulsory keywords
 LAMBDA the lambda parameter is needed for smoothing, is in the units of plumed REFERENCE the pdb is needed to provide the various milestones PROPERTY the property to be used in the indexing: this goes in the REMARK field of the reference
Options
 NUMERICAL_DERIVATIVES ( default=off ) calculate the derivatives for these quantities numerically NOPBC ( default=off ) ignore the periodic boundary conditions when calculating distances NEIGH_SIZE size of the neighbor list NEIGH_STRIDE how often the neighbor list needs to be calculated in time units EPSILON (default=-1) the maximum distance between the close and the current structure, the positive value turn on the close structure method LOG_CLOSE (default=0) value 1 enables logging regarding the close structure DEBUG_CLOSE (default=0) value 1 enables extensive debugging info regarding the close structure, the simulation will run much slower