PATHMSD

This is part of the colvar module

This Colvar calculates path collective variables.

This is the Path Collective Variables implementation ( see [23] ). 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.

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

Click on the labels of the actions for more information on what each action computes

p1: PATHMSD 
REFERENCE
compulsory keyword 
the pdb is needed to provide the various milestones 
=file.pdb 
LAMBDA
compulsory keyword 
the lambda parameter is needed for smoothing, is in the units of plumed 
=500.0 
NEIGH_STRIDE
how often the neighbor list needs to be calculated in time units 
=4 
NEIGH_SIZE
size of the neighbor list 
=8 The PATHMSD action with label p1 calculates the following quantities:

 Quantity   
 Description  
p1.sss
the position on the path
p1.zzz
the distance from the path


PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=p1.sss,p1.zzz 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=1 
FILE
the name of the file on which to output these quantities 
=colvar 
FMT
the format that should be used to output real numbers 
=%8.4f The PRINT action with label 

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.

Glossary of keywords and components

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