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| 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 [55]. 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 ammount by which a set of collective variables change. As such this implementation of the propertymap 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.
| 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 | the value of the lambda parameter for paths |
| NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |
| SERIAL | ( default=off ) do the calculation in serial. Do not parallelize |
| 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 |
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.
p2: GPROPERTYMAP REFERENCE=allv.pdb PROPERTY=X,Y LAMBDA=69087 PRINT ARG=p2.X,p2.Y,p2.zpath STRIDE=1 FILE=colvar
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
1.8.14