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| This is part of the colvar module |
This Colvar calculates path collective variables.
This is the Path Collective Variables implementation ( see [10] ). This variable computes the progress along a given set of frames that is provided in input ("sss" component) and the distance from them ("zzz" component). (see below).
By default this Action calculates the following quantities. These quanties can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.
| Quantity | Description |
| sss | the position on the path |
| zzz | the distance from the path |
| LAMBDA | the lambda parameter is needed for smoothing, is in the units of plumed |
| REFERENCE | the pdb is needed to provide the various milestones |
| 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 |
Here below is a case where you have defined three frames and you want to calculate the progress along the path and the distance from it in p1
p1: PATHMSD REFERENCE=file.pdb LAMBDA=500.0 NEIGH_STRIDE=4 NEIGH_SIZE=8 PRINT ARG=p1.sss,p1.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 the REFERENCE PDB file the frames must be separated either using END or ENDMDL.
1.8.10 
