GPROPERTYMAP

	This is part of the mapping module
	It is only available if you configure PLUMED with ./configure –enable-modules=mapping . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

Property maps but with a more flexible framework for the distance metric being used.

This colvar calculates a property map using the formalism developed by Spiwok [99]. In essence if you have the value of some property, \(X_i\), that it takes at a set of high-dimensional positions then you calculate the value of the property at some arbitrary point in the high-dimensional space using:

\[ X=\frac{\sum_i X_i*\exp(-\lambda D_i(x))}{\sum_i \exp(-\lambda D_i(x))} \]

Within PLUMED there are multiple ways to define the distance from a high-dimensional configuration, \(D_i\). You could calculate the RMSD distance or you could calculate the amount by which a set of collective variables change. As such this implementation of the property map allows one to use all the different distance metric that are discussed in Distances from reference configurations. This is as opposed to the alternative implementation PROPERTYMAP which is a bit faster but which only allows one to use the RMSD distance.

Examples

The input shown below can be used to calculate the interpolated values of two properties called X and Y based on the values that these properties take at a set of reference configurations and using the formula above. For this input the distances between the reference configurations and the instantaneous configurations are calculated using the OPTIMAL metric that is discussed at length in the manual pages on RMSD.

Click on the labels of the actions for more information on what each action computes

p2: GPROPERTYMAP 
REFERENCE
compulsory keyword 
a pdb file containing the set of reference configurations 
=allv.pdb 
PROPERTY
the property to be used in the index. 
=X,Y 
LAMBDA
compulsory keyword 
the lambda parameter is needed for smoothing, is in the units of plumed 
=69087  You cannot view the components that are calculated by each action for this input file. Sorry 
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=p2.X,p2.Y,p2.zpath 
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  You cannot view the components that are calculated by each action for this input file. Sorry 

The additional input file for this calculation, which contains the reference frames and the values of X and Y at these reference points has the following format.

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
ATOM      6  OL  ALA     1      -1.177  -0.889   2.401  1.00  1.00
ATOM      7  NL  ALA     1      -1.313   0.341   0.529  1.00  1.00
ATOM      8  HL  ALA     1      -1.845   0.961  -0.011  1.00  1.00
ATOM      9  CA  ALA     1      -0.003  -0.019   0.021  1.00  1.00
ATOM     10  HA  ALA     1       0.205  -1.051   0.259  1.00  1.00
ATOM     11  CB  ALA     1       0.009   0.135  -1.509  1.00  1.00
ATOM     15  CRP ALA     1       1.121   0.799   0.663  1.00  1.00
ATOM     16  OR  ALA     1       1.723   1.669   0.043  1.00  1.00
ATOM     17  NR  ALA     1       1.423   0.519   1.941  1.00  1.00
ATOM     18  HR  ALA     1       0.873  -0.161   2.413  1.00  1.00
ATOM     19  CR  ALA     1       2.477   1.187   2.675  1.00  1.00
END
FIXED
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
ATOM      6  OL  ALA     1      -1.201  -0.849   2.425  1.00  1.00
ATOM      7  NL  ALA     1      -1.296   0.337   0.534  1.00  1.00
ATOM      8  HL  ALA     1      -1.807   0.951  -0.044  1.00  1.00
ATOM      9  CA  ALA     1       0.009  -0.067   0.033  1.00  1.00
ATOM     10  HA  ALA     1       0.175  -1.105   0.283  1.00  1.00
ATOM     11  CB  ALA     1       0.027   0.046  -1.501  1.00  1.00
ATOM     15  CRP ALA     1       1.149   0.725   0.654  1.00  1.00
ATOM     16  OR  ALA     1       1.835   1.491  -0.011  1.00  1.00
ATOM     17  NR  ALA     1       1.380   0.537   1.968  1.00  1.00
ATOM     18  HR  ALA     1       0.764  -0.060   2.461  1.00  1.00
ATOM     19  CR  ALA     1       2.431   1.195   2.683  1.00  1.00
END

Glossary of keywords and components

Description of components

Quantity	Keyword	Description
gspath	GPATH	the position along the path calculated using the geometric formula
gzpath	GPATH	the distance from the path calculated using the geometric formula
spath	GPATH	the position along the path calculated using the geometric formula
zpath	GPATH	the distance from the path calculated using the geometric formula

Compulsory keywords

REFERENCE	a pdb file containing the set of reference configurations
TYPE	( default=OPTIMAL-FAST ) the manner in which distances are calculated. More information on the different metrics that are available in PLUMED can be found in the section of the manual on Distances from reference configurations
LAMBDA	the lambda parameter is needed for smoothing, is in the units of plumed

Options

NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
NOSPATH	( default=off ) do not calculate the spath CV
NOZPATH	( default=off ) do not calculate the zpath CV
GPATH	( default=off ) calculate the trigonometric path
ARG	the list of arguments you would like to use in your definition of the path
COEFFICIENTS	the coefficients of the displacements along each argument that should be used when calculating the euclidean distance
PROPERTY	the property to be used in the index. This should be in the REMARK of the reference