GPROPERTYMAP

This is part of the mapping module

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 [123]. 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 REFERENCEcompulsory keyword 
a pdb file containing the set of reference configurations =allv.pdb PROPERTYcompulsory keyword 
the property to be used in the index. =X,Y LAMBDAcompulsory keyword ( default=0 )
the value of the lambda parameter for paths =69087 The GPROPERTYMAP action with label p2 calculates the following quantities:

 Quantity   
 Description  
p2.zpath
the label of this action is set by user in the input. See documentation above.
p2.X
the label of this action is set by user in the input. See documentation above.
p2.Y
the label of this action is set by user in the input. See documentation above.


PRINT ARGthe input for this action is the scalar output from one or more other actions. =p2.X,p2.Y,p2.zpath 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 The PRINT action with label 

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

Compulsory keywords

REFERENCE	a pdb file containing the set of reference configurations
PROPERTY	the property to be used in the index. This should be in the REMARK of the reference
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	( default=0 ) the value of the lambda parameter for paths

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
SERIAL	( default=off ) do the calculation in serial. Do not use MPI
LOWMEM	( default=off ) lower the memory requirements
TIMINGS	( default=off ) output information on the timings of the various parts of the calculation
DISABLE_CHECKS	( default=off ) disable checks on reference input structures.
NOZPATH	( default=off ) do not calculate the zpath position
NOMAPPING	( default=off ) do not calculate the position on the manifold