PATHMSD
 This is part of the colvar module

This Colvar calculates path collective variables.

This is the Path Collective Variables implementation ( see [21] ). 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).

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 with 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.

Description of components

By default this Action calculates the following quantities. These quantities 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
Compulsory keywords
 LAMBDA the lambda parameter is needed for smoothing, is in the units of plumed REFERENCE the pdb is needed to provide the various milestones
Options
 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
Examples

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 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.

This input must be accompanied by a REFERENCE PDB file in which the positions of each of the frames are specified separated using either END or ENDMDL as shown below:

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
END
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
END
ATOM      1  CL  ALA     1      -2.990   0.383   2.277  1.00  1.00
ATOM      5  CLP ALA     1      -1.664  -0.085   1.831  1.00  1.00
ATOM      6  OL  ALA     1      -0.987  -0.835   2.533  1.00  1.00
ATOM      7  NL  ALA     1      -1.227   0.364   0.646  1.00  1.00
END

Note
The implementation of this collective variable and of PROPERTYMAP is shared, as well as most input options.