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 [45] [82] 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.

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 \(i\)th 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.
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.

PIV ...
LABEL=Pivd1
PRECISION=1000
NLIST
REF_FILE=Ref1.pdb
PIVATOMS=3
ATOMTYPES=A,B,C
SFACTOR=0.3,0.5,1.0,0.2,0.2,0.2
SORT=1,1,1,1,1,1
SWITCH1={RATIONAL R_0=0.6 MM=12 NN=4}
SWITCH2={RATIONAL R_0=0.4 MM=10 NN=5}
SWITCH3={RATIONAL R_0=0.4 MM=10 NN=5}
SWITCH4={RATIONAL R_0=0.5 MM=12 NN=6}
SWITCH5={RATIONAL R_0=0.5 MM=12 NN=6}
SWITCH6={RATIONAL R_0=0.5 MM=12 NN=6}
NL_CUTOFF=0.8,0.6,0.6,0.7,0.7,0.7
NL_STRIDE=10,10,10,10,10,10
NL_SKIN=0.1,0.1,0.1,0.1,0.1,0.1
... PIV
PIV ...
LABEL=Pivd2
PRECISION=1000
NLIST
REF_FILE=Ref2.pdb
PIVATOMS=3
ATOMTYPES=A,B,C
SFACTOR=0.3,0.5,1.0,0.2,0.2,0.2
SORT=1,1,1,1,1,1
SWITCH1={RATIONAL R_0=0.6 MM=12 NN=4}
SWITCH2={RATIONAL R_0=0.4 MM=10 NN=5}
SWITCH3={RATIONAL R_0=0.4 MM=10 NN=5}
SWITCH4={RATIONAL R_0=0.5 MM=12 NN=6}
SWITCH5={RATIONAL R_0=0.5 MM=12 NN=6}
SWITCH6={RATIONAL R_0=0.5 MM=12 NN=6}
NL_CUTOFF=0.8,0.6,0.6,0.7,0.7,0.7
NL_STRIDE=10,10,10,10,10,10
NL_SKIN=0.1,0.1,0.1,0.1,0.1,0.1
... PIV
PIV ...
LABEL=Pivd3
PRECISION=1000
NLIST
REF_FILE=Ref3.pdb
PIVATOMS=3
ATOMTYPES=A,B,C
SFACTOR=0.3,0.5,1.0,0.2,0.2,0.2
SORT=1,1,1,1,1,1
SWITCH1={RATIONAL R_0=0.6 MM=12 NN=4}
SWITCH2={RATIONAL R_0=0.4 MM=10 NN=5}
SWITCH3={RATIONAL R_0=0.4 MM=10 NN=5}
SWITCH4={RATIONAL R_0=0.5 MM=12 NN=6}
SWITCH5={RATIONAL R_0=0.5 MM=12 NN=6}
SWITCH6={RATIONAL R_0=0.5 MM=12 NN=6}
NL_CUTOFF=0.8,0.6,0.6,0.7,0.7,0.7
NL_STRIDE=10,10,10,10,10,10
NL_SKIN=0.1,0.1,0.1,0.1,0.1,0.1
... PIV

PRINT ARG=Pivd1,Pivd2,Pivd3 FILE=colvar

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.

PIV ...
LABEL=c1
PRECISION=1000
VOLUME=12.15
NLIST
REF_FILE=Ref1.pdb
PIVATOMS=2
ATOMTYPES=A,B
ONLYDIRECT
SFACTOR=1.0,0.2
SORT=1,1
SWITCH1={RATIONAL R_0=0.6 MM=12 NN=4}
SWITCH2={RATIONAL R_0=0.5 MM=10 NN=5}
NL_CUTOFF=1.2,1.2
NL_STRIDE=10,10
NL_SKIN=0.1,0.1
... PIV
PIV ...
LABEL=c2
PRECISION=1000
VOLUME=12.15
NLIST
REF_FILE=Ref2.pdb
PIVATOMS=2
ATOMTYPES=A,B
ONLYDIRECT
SFACTOR=1.0,0.2
SORT=1,1
SWITCH1={RATIONAL R_0=0.6 MM=12 NN=4}
SWITCH2={RATIONAL R_0=0.4 MM=10 NN=5}
NL_CUTOFF=1.2,1.2
NL_STRIDE=10,10
NL_SKIN=0.1,0.1
... PIV

p1: FUNCPATHMSD ARG=c1,c2 LAMBDA=0.180338
METAD ARG=p1.s,p1.z SIGMA=0.01,0.2 HEIGHT=0.8 PACE=500   LABEL=res
PRINT ARG=c1,c2,p1.s,p1.z,res.bias STRIDE=500  FILE=colvar FMT=%15.6f

When using PIV please cite [82] .

(See also PRINT)