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
tested on master
p3: PROPERTYMAP 
REFERENCE
compulsory keyword the pdb is needed to provide the various milestones
=allv.pdb
PROPERTY
compulsory keyword the property to be used in the indexing: this goes in the REMARK field of the reference
=X,Y
LAMBDA
compulsory keyword the lambda parameter is needed for smoothing, is in the units of plumed
=69087
NEIGH_SIZE
size of the neighbor list
=8
NEIGH_STRIDE
how often the neighbor list needs to be calculated in time units
=4 PRINT
ARG
the input for this action is the scalar output from one or more other actions.
=p3.X,p3.Y,p3.zzz
STRIDE
compulsory keyword ( default=1 ) the frequency with which the quantities of interest should be output
=1
FILE
the name of the file on which to output these quantities
=colvar
FMT
the 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