This is part of the colvar module

Calculate generic property maps.

This Colvar calculates the property maps according to the work of Spiwok [79].

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).

Warning: 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

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
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
LOG_CLOSE	same as LOG-CLOSE
DEBUG_CLOSE	same as DEBUG-CLOSE

Examples

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.

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.