This is part of the colvar module

Calculate generic property maps.

This Colvar calculates the property maps according to the work of Spiwok [55].

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 MSD after optimal alignment calculated on the pdb frames you input (see Kearsley).

The molecule used for 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 WHOLEMOLECULES to reconstruct it before PROPERTYMAP calculation.
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 these customizable components 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

( default=off ) calculate the derivatives for these quantities numerically

NEIGH_SIZE size of the neighbor list

how often the neighbor list needs to be calculated in time units

p3: PROPERTYMAP REFERENCE=../../trajectories/path_msd/allv.pdb PROPERTY=X,Y LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=4
PRINT ARG=p3.X,p3.Y,p3.zzz STRIDE=1 FILE=colvar FMT=%8.4f

note that NEIGH_STRIDE=4 NEIGH_SIZE=8 control the neighborlist parameter (optional but recommended for performance) and states that the neighbor list will be calculated every 4 timesteps 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.

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
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
The implementation of this collective variable and of PATHMSD is shared, as well as most input options.