PIV

	This is part of the piv module
	It is only available if you configure PLUMED with ./configure –enable-modules=piv . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

Calculates the PIV-distance.

PIV distance is the squared Cartesian distance between the PIV [42] [91] associated to the configuration of the system during the dynamics and a reference configuration provided as input (PDB file format). PIV can be used together with FUNCPATHMSD to define a path in the PIV space.

Examples

The following example calculates PIV-distances from three reference configurations in Ref1.pdb, Ref2.pdb and Ref3.pdb and prints the results in a file named colvar. Three atoms (PIVATOMS=3) with names (pdb file) A B and C are used to construct the PIV and all PIV blocks (AA, BB, CC, AB, AC, BC) are considered. SFACTOR is a scaling factor that multiplies the contribution to the PIV-distance given by the single PIV block. NLIST sets the use of neighbor lists for calculating atom-atom distances. The SWITCH keyword specifies the parameters of the switching function that transforms atom-atom distances. SORT=1 means that the PIV block elements are sorted (SORT=0 no sorting.) Values for SORT, SFACTOR and the neighbor list parameters have to be specified for each block. The order is the following: AA,BB,CC,AB,AC,BC. If ONLYDIRECT (ONLYCROSS) is used the order is AA,BB,CC (AB,AC,BC). The sorting operation within each PIV block is performed using the counting sort algorithm, PRECISION specifies the size of the counting array.

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

Pivd1: 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 ith reference structure. 
=Ref1.pdb 
   
PIVATOMS
compulsory keyword 
Number of atoms to use for PIV. 
=3 
   
ATOMTYPES
compulsory keyword 
The atom types to use for PIV. 
=A,B,C 
   
SFACTOR
Scale the PIV-distance by such block-specific factor 
=0.3,0.5,1.0,0.2,0.2,0.2 
   
SORT
compulsory keyword 
Whether to sort or not the PIV block. 
=1,1,1,1,1,1 
   
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}  
   
SWITCH3
compulsory keyword 
The switching functions parameter.You 
={RATIONAL R_0=0.4 MM=10 NN=5}  
   
SWITCH4
compulsory keyword 
The switching functions parameter.You 
={RATIONAL R_0=0.5 MM=12 NN=6}  
   
SWITCH5
compulsory keyword 
The switching functions parameter.You 
={RATIONAL R_0=0.5 MM=12 NN=6}  
   
SWITCH6
compulsory keyword 
The switching functions parameter.You 
={RATIONAL R_0=0.5 MM=12 NN=6}  
   
NL_CUTOFF
Neighbor lists cutoff. 
=0.8,0.6,0.6,0.7,0.7,0.7 
   
NL_STRIDE
Update neighbor lists every NL_STRIDE steps. 
=10,10,10,10,10,10 
   
NL_SKIN
The maximum atom displacement tolerated for the neighbor lists update. 
=0.1,0.1,0.1,0.1,0.1,0.1 
... You cannot view the components that are calculated by each action for this input file. Sorry 
Pivd2: 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 ith reference structure. 
=Ref2.pdb 
   
PIVATOMS
compulsory keyword 
Number of atoms to use for PIV. 
=3 
   
ATOMTYPES
compulsory keyword 
The atom types to use for PIV. 
=A,B,C 
   
SFACTOR
Scale the PIV-distance by such block-specific factor 
=0.3,0.5,1.0,0.2,0.2,0.2 
   
SORT
compulsory keyword 
Whether to sort or not the PIV block. 
=1,1,1,1,1,1 
   
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}  
   
SWITCH3
compulsory keyword 
The switching functions parameter.You 
={RATIONAL R_0=0.4 MM=10 NN=5}  
   
SWITCH4
compulsory keyword 
The switching functions parameter.You 
={RATIONAL R_0=0.5 MM=12 NN=6}  
   
SWITCH5
compulsory keyword 
The switching functions parameter.You 
={RATIONAL R_0=0.5 MM=12 NN=6}  
   
SWITCH6
compulsory keyword 
The switching functions parameter.You 
={RATIONAL R_0=0.5 MM=12 NN=6}  
   
NL_CUTOFF
Neighbor lists cutoff. 
=0.8,0.6,0.6,0.7,0.7,0.7 
   
NL_STRIDE
Update neighbor lists every NL_STRIDE steps. 
=10,10,10,10,10,10 
   
NL_SKIN
The maximum atom displacement tolerated for the neighbor lists update. 
=0.1,0.1,0.1,0.1,0.1,0.1 
... You cannot view the components that are calculated by each action for this input file. Sorry 
Pivd3: 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 ith reference structure. 
=Ref3.pdb 
   
PIVATOMS
compulsory keyword 
Number of atoms to use for PIV. 
=3 
   
ATOMTYPES
compulsory keyword 
The atom types to use for PIV. 
=A,B,C 
   
SFACTOR
Scale the PIV-distance by such block-specific factor 
=0.3,0.5,1.0,0.2,0.2,0.2 
   
SORT
compulsory keyword 
Whether to sort or not the PIV block. 
=1,1,1,1,1,1 
   
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}  
   
SWITCH3
compulsory keyword 
The switching functions parameter.You 
={RATIONAL R_0=0.4 MM=10 NN=5}  
   
SWITCH4
compulsory keyword 
The switching functions parameter.You 
={RATIONAL R_0=0.5 MM=12 NN=6}  
   
SWITCH5
compulsory keyword 
The switching functions parameter.You 
={RATIONAL R_0=0.5 MM=12 NN=6}  
   
SWITCH6
compulsory keyword 
The switching functions parameter.You 
={RATIONAL R_0=0.5 MM=12 NN=6}  
   
NL_CUTOFF
Neighbor lists cutoff. 
=0.8,0.6,0.6,0.7,0.7,0.7 
   
NL_STRIDE
Update neighbor lists every NL_STRIDE steps. 
=10,10,10,10,10,10 
   
NL_SKIN
The maximum atom displacement tolerated for the neighbor lists update. 
=0.1,0.1,0.1,0.1,0.1,0.1 
... You cannot view the components that are calculated by each action for this input file. Sorry 
PRINT 
ARG
compulsory keyword 
the labels of the values that you would like to print to the file 
=Pivd1,Pivd2,Pivd3 
FILE
the name of the file on which to output these quantities 
=colvar  You cannot view the components that are calculated by each action for this input file. Sorry 

WARNING: Both the "CRYST" and "ATOM" lines of the PDB files must conform precisely to the official pdb format, including the width of each alphanumerical field:

CRYST1   31.028   36.957   23.143  89.93  92.31  89.99 P 1           1
ATOM      1  OW1 wate    1      15.630  19.750   1.520  1.00  0.00

In each pdb frame, atoms must be numbered in the same order and with the same element symbol as in the input of the MD program.

The following example calculates the PIV-distances from two reference configurations Ref1.pdb and Ref2.pdb and uses PIV-distances to define a Path Collective Variable (FUNCPATHMSD) with only two references (Ref1.pdb and Ref2.pdb). With the VOLUME keyword one scales the atom-atom distances by the cubic root of the ratio between the specified value and the box volume of the initial step of the trajectory file.

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 
   
VOLUME
Scale atom-atom distances by the cubic root of the cell volume. 
=12.15 
   
NLIST
( default=off ) Use a neighbor list for distance calculations. 
 
   
REF_FILE
compulsory keyword 
PDB file name that contains the ith 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 
   
VOLUME
Scale atom-atom distances by the cubic root of the cell volume. 
=12.15 
   
NLIST
( default=off ) Use a neighbor list for distance calculations. 
 
   
REF_FILE
compulsory keyword 
PDB file name that contains the ith 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
compulsory keyword 
the labels of the values from which the function is calculated 
=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
compulsory keyword 
the labels of the scalars on which the bias will act 
=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
compulsory keyword 
the labels of the values that you would like to print to the file 
=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 

When using PIV please cite [91] .

(See also PRINT)

Glossary of keywords and components

Description of components

By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. 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
.#!value	the PIV-distance

Compulsory keywords

SWITCH	The switching functions parameter.You should specify a Switching function for all PIV blocks.Details of the various switching functions you can use are provided on switchingfunction.. You can use multiple instances of this keyword i.e. SWITCH1, SWITCH2, SWITCH3...
PRECISION	the precision for approximating reals with integers in sorting.
REF_FILE	PDB file name that contains the ith reference structure.
PIVATOMS	Number of atoms to use for PIV.
SORT	Whether to sort or not the PIV block.
ATOMTYPES	The atom types to use for PIV.

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
TEST	( default=off ) Print the actual and reference PIV and exit
COM	( default=off ) Use centers of mass of groups of atoms instead of atoms as specified in the Pdb file
ONLYCROSS	( default=off ) Use only cross-terms (A-B, A-C, B-C, ...) in PIV
ONLYDIRECT	( default=off ) Use only direct-terms (A-A, B-B, C-C, ...) in PIV
DERIVATIVES	( default=off ) Activate the calculation of the PIV for every class (needed for numerical derivatives).
NLIST	( default=off ) Use a neighbor list for distance calculations.
SERIAL	( default=off ) Perform the calculation in serial - for debug purpose
TIMER	( default=off ) Perform timing analysis on heavy loops.
SFACTOR	Scale the PIV-distance by such block-specific factor
VOLUME	Scale atom-atom distances by the cubic root of the cell volume. The input volume is used to scale the R_0 value of the switching function.
UPDATEPIV	Frequency (in steps) at which the PIV is updated.
NL_CUTOFF	Neighbor lists cutoff.
NL_STRIDE	Update neighbor lists every NL_STRIDE steps.
NL_SKIN	The maximum atom displacement tolerated for the neighbor lists update.