FUNCPATHMSD

This is part of the function module

This function calculates path collective variables.

This is the Path Collective Variables implementation ( see [24] ). This variable computes the progress along a given set of frames that is provided in input ("s" component) and the distance from them ("z" component). It is a function of mean squared displacement that are obtained by the joint use of mean squared displacement variables with the SQUARED flag (see below).

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

contract shortcuts

t1: RMSD 
REFERENCE
compulsory keyword 
a file in pdb format containing the reference structure and the atoms involved in
the CV 
=frame_1.pdb 
TYPE
compulsory keyword ( default=SIMPLE )
the manner in which RMSD alignment is performed. 
=OPTIMAL 
SQUARED
( default=off ) This should be setted if you want MSD instead of RMSD 
 The RMSD action with label t1 calculates a single scalar value
t2: RMSD 
REFERENCE
compulsory keyword 
a file in pdb format containing the reference structure and the atoms involved in
the CV 
=frame_21.pdb 
TYPE
compulsory keyword ( default=SIMPLE )
the manner in which RMSD alignment is performed. 
=OPTIMAL 
SQUARED
( default=off ) This should be setted if you want MSD instead of RMSD 
 The RMSD action with label t2 calculates a single scalar value
t3: RMSD 
REFERENCE
compulsory keyword 
a file in pdb format containing the reference structure and the atoms involved in
the CV 
=frame_42.pdb 
TYPE
compulsory keyword ( default=SIMPLE )
the manner in which RMSD alignment is performed. 
=OPTIMAL 
SQUARED
( default=off ) This should be setted if you want MSD instead of RMSD 
 The RMSD action with label t3 calculates a single scalar value
p1: FUNCPATHMSD 
ARG
the input for this action is the scalar output from one or more other actions. 
=t1,t2,t3 
LAMBDA
compulsory keyword 
the lambda parameter is needed for smoothing, is in the units of plumed 
=500.0 The FUNCPATHMSD action with label p1 calculates the following quantities:

 Quantity   
 Description  
p1.s
the position on the path
p1.z
the distance from the path


For this input you would then define the position of the reference coordinates in three separate pdb files. The contents of the file frame_1.pdb are 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
ATOM      8  HL  ALA     1      -1.845   0.961  -0.011  1.00  1.00
END
This is then frame.21.pdb:
ATOM      1  CL  ALA     1      -3.089   1.850   1.546  1.00  1.00
ATOM      5  CLP ALA     1      -1.667   1.457   1.629  1.00  1.00
ATOM      6  OL  ALA     1      -0.974   1.868   2.533  1.00  1.00
ATOM      7  NL  ALA     1      -1.204   0.683   0.642  1.00  1.00
ATOM      8  HL  ALA     1      -1.844   0.360  -0.021  1.00  1.00
END
and finally this is frame_42.pdb:
ATOM      1  CL  ALA     1      -3.257   1.605   1.105  1.00  1.00
ATOM      5  CLP ALA     1      -1.941   1.459   0.447  1.00  1.00
ATOM      6  OL  ALA     1      -1.481   2.369  -0.223  1.00  1.00
ATOM      7  NL  ALA     1      -1.303   0.291   0.647  1.00  1.00
ATOM      8  HL  ALA     1      -1.743  -0.379   1.229  1.00  1.00
END
This second example shows how to define a PATH in CONTACTMAP space:

 Click on the labels of the actions for more information on what each action computes 
c1: CONTACTMAP ...
   
ATOMS1
the atoms involved in each of the contacts you wish to calculate. 
=1,2 
REFERENCE1
A reference value for a given contact, by default is 0.0 
=0.1 
   
ATOMS2
the atoms involved in each of the contacts you wish to calculate. 
=3,4 
REFERENCE2
A reference value for a given contact, by default is 0.0 
=0.5 
   
ATOMS3
the atoms involved in each of the contacts you wish to calculate. 
=4,5 
REFERENCE3
A reference value for a given contact, by default is 0.0 
=0.25 
   
ATOMS4
the atoms involved in each of the contacts you wish to calculate. 
=5,6 
REFERENCE4
A reference value for a given contact, by default is 0.0 
=0.0 
   
SWITCH
compulsory keyword 
The switching functions to use for each of the contacts in your map. 
={RATIONAL R_0=1.5}  
   
   
CMDIST
( default=off ) calculate the distance with respect to the provided reference contact
map 
 
...The CONTACTMAP action with label c1 calculates a single scalar value
c2: CONTACTMAP ...
   
ATOMS1
the atoms involved in each of the contacts you wish to calculate. 
=1,2 
REFERENCE1
A reference value for a given contact, by default is 0.0 
=0.3 
   
ATOMS2
the atoms involved in each of the contacts you wish to calculate. 
=3,4 
REFERENCE2
A reference value for a given contact, by default is 0.0 
=0.9 
   
ATOMS3
the atoms involved in each of the contacts you wish to calculate. 
=4,5 
REFERENCE3
A reference value for a given contact, by default is 0.0 
=0.45 
   
ATOMS4
the atoms involved in each of the contacts you wish to calculate. 
=5,6 
REFERENCE4
A reference value for a given contact, by default is 0.0 
=0.1 
   
SWITCH
compulsory keyword 
The switching functions to use for each of the contacts in your map. 
={RATIONAL R_0=1.5}  
   
   
CMDIST
( default=off ) calculate the distance with respect to the provided reference contact
map 
 
...The CONTACTMAP action with label c2 calculates a single scalar value
c3: CONTACTMAP ...
   
ATOMS1
the atoms involved in each of the contacts you wish to calculate. 
=1,2 
REFERENCE1
A reference value for a given contact, by default is 0.0 
=1.0 
   
ATOMS2
the atoms involved in each of the contacts you wish to calculate. 
=3,4 
REFERENCE2
A reference value for a given contact, by default is 0.0 
=1.0 
   
ATOMS3
the atoms involved in each of the contacts you wish to calculate. 
=4,5 
REFERENCE3
A reference value for a given contact, by default is 0.0 
=1.0 
   
ATOMS4
the atoms involved in each of the contacts you wish to calculate. 
=5,6 
REFERENCE4
A reference value for a given contact, by default is 0.0 
=1.0 
   
SWITCH
compulsory keyword 
The switching functions to use for each of the contacts in your map. 
={RATIONAL R_0=1.5}  
   
   
CMDIST
( default=off ) calculate the distance with respect to the provided reference contact
map 
 
...The CONTACTMAP action with label c3 calculates a single scalar value
p1: FUNCPATHMSD 
ARG
the input for this action is the scalar output from one or more other actions. 
=c1,c2,c3 
LAMBDA
compulsory keyword 
the lambda parameter is needed for smoothing, is in the units of plumed 
=500.0 The FUNCPATHMSD action with label p1 calculates the following quantities:

 Quantity   
 Description  
p1.s
the position on the path
p1.z
the distance from the path


This third example shows how to define a PATH in PIV space:

 Click on the labels of the actions for more information on what each action computes 
c1: PIV ...
   
   
PRECISION
compulsory keyword 
the precision for approximating reals with integers in sorting. 
=1000 
   
NLIST
( default=off ) Use a neighbor list for distance calculations. 
 
   
REF_FILE
compulsory keyword 
PDB file name that contains the \f$i\f$th reference structure. 
=Ref1.pdb 
   
PIVATOMS
compulsory keyword 
Number of atoms to use for PIV. 
=2 
   
ATOMTYPES
compulsory keyword 
The atom types to use for PIV. 
=A,B 
   
ONLYDIRECT
( default=off ) Use only direct-terms (A-A, B-B, C-C, ...) 
 
   
SFACTOR
Scale the PIV-distance by such block-specific factor 
=1.0,0.2 
   
SORT
compulsory keyword 
Whether to sort or not the PIV block. 
=1,1 
   
SWITCH1
compulsory keyword 
The switching functions parameter.You 
={RATIONAL R_0=0.6 MM=12 NN=4}  
   
SWITCH2
compulsory keyword 
The switching functions parameter.You 
={RATIONAL R_0=0.5 MM=10 NN=5}  
   
NL_CUTOFF
Neighbor lists cutoff. 
=1.2,1.2 
   
NL_STRIDE
Update neighbor lists every NL_STRIDE steps. 
=10,10 
   
NL_SKIN
The maximum atom displacement tolerated for the neighbor lists update. 
=0.1,0.1 
... You cannot view the components that are calculated by each action for this input file. Sorry 
c2: PIV ...
   
   
PRECISION
compulsory keyword 
the precision for approximating reals with integers in sorting. 
=1000 
   
NLIST
( default=off ) Use a neighbor list for distance calculations. 
 
   
REF_FILE
compulsory keyword 
PDB file name that contains the \f$i\f$th reference structure. 
=Ref2.pdb 
   
PIVATOMS
compulsory keyword 
Number of atoms to use for PIV. 
=2 
   
ATOMTYPES
compulsory keyword 
The atom types to use for PIV. 
=A,B 
   
ONLYDIRECT
( default=off ) Use only direct-terms (A-A, B-B, C-C, ...) 
 
   
SFACTOR
Scale the PIV-distance by such block-specific factor 
=1.0,0.2 
   
SORT
compulsory keyword 
Whether to sort or not the PIV block. 
=1,1 
   
SWITCH1
compulsory keyword 
The switching functions parameter.You 
={RATIONAL R_0=0.6 MM=12 NN=4}  
   
SWITCH2
compulsory keyword 
The switching functions parameter.You 
={RATIONAL R_0=0.4 MM=10 NN=5}  
   
NL_CUTOFF
Neighbor lists cutoff. 
=1.2,1.2 
   
NL_STRIDE
Update neighbor lists every NL_STRIDE steps. 
=10,10 
   
NL_SKIN
The maximum atom displacement tolerated for the neighbor lists update. 
=0.1,0.1 
... You cannot view the components that are calculated by each action for this input file. Sorry 
p1: FUNCPATHMSD 
ARG
the input for this action is the scalar output from one or more other actions. 
=c1,c2 
LAMBDA
compulsory keyword 
the lambda parameter is needed for smoothing, is in the units of plumed 
=0.180338  You cannot view the components that are calculated by each action for this input file. Sorry 
res: METAD 
ARG
the input for this action is the scalar output from one or more other actions. 
=p1.s,p1.z 
SIGMA
compulsory keyword 
the widths of the Gaussian hills 
=0.01,0.2 
HEIGHT
the heights of the Gaussian hills. 
=0.8 
PACE
compulsory keyword 
the frequency for hill addition 
=500  You cannot view the components that are calculated by each action for this input file. Sorry 
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=c1,c2,p1.s,p1.z,res.bias 
STRIDE
compulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output 
=500 
FILE
the name of the file on which to output these quantities 
=colvar 
FMT
the format that should be used to output real numbers 
=%15.6f  You cannot view the components that are calculated by each action for this input file. Sorry 

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    

 s  
the position on the path   

 z  
the distance from the path   

Compulsory keywords



 LAMBDA  
the lambda parameter is needed for smoothing, is in the units of plumed   

Options



 NUMERICAL_DERIVATIVES  
( default=off ) calculate the derivatives for these quantities numerically  



 ARG  
the input for this action is the scalar output from one or more other actions. The particular scalars that you will use are referenced using the label of the action. If the label appears on its own then it is assumed that the Action calculates a single scalar value. The value of this scalar is thus used as the input to this new action. If * or *.* appears the scalars calculated by all the proceeding actions in the input file are taken. Some actions have multi-component outputs and each component of the output has a specific label. For example a DISTANCE action labelled dist may have three components x, y and z. To take just the x component you should use dist.x, if you wish to take all three components then use dist.*.More information on the referencing of Actions can be found in the section of the manual on the PLUMED Getting Started. Scalar values can also be referenced using POSIX regular expressions as detailed in the section on Regular Expressions. To use this feature you you must compile PLUMED with the appropriate flag.. You can use multiple instances of this keyword i.e. ARG1, ARG2, ARG3...   

 NEIGH_SIZE  
size of the neighbor list   

 NEIGH_STRIDE  
how often the neighbor list needs to be calculated in time units