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| This is part of the colvar module |
Calculate generic property maps.
This Colvar calculates the property maps according to the work of Spiwok [89].
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 mean squared displacement after optimal alignment calculated on the pdb frames you input (see Kearsley).
When running with periodic boundary conditions, the atoms should be in the proper periodic image. This is done automatically since PLUMED 2.5, by considering the ordered list of atoms and rebuilding molecules using a procedure that is equivalent to that done in WHOLEMOLECULES . Notice that rebuilding is local to this action. This is different from WHOLEMOLECULES which actually modifies the coordinates stored in PLUMED.
In case you want to recover the old behavior you should use the NOPBC flag. In that case you need to take care that atoms are in the correct periodic image.
The names of the components in this action can be customized by the user in the actions input file. However, in addition to the components that can be customized the following quantities will always be output
| Quantity | Description |
| zzz | the minimum distance from the reference points |
| 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 |
| NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |
| NOPBC | ( default=off ) ignore the periodic boundary conditions when calculating distances |
| 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 |
p3: PROPERTYMAP REFERENCE=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 neighbor list parameter (optional but recommended for performance) and states that the neighbor list will be calculated every 4 steps 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
1.8.14