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PIV_distance.md

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Associating PIVs to system configurations

The following example shows how to associate a PIV to a system configuration:

PIV ...
LABEL=c1
PIVATOMS=1
ATOMTYPES=O
PRECISION=1000
REF_FILE=Liq.pdb
SORT=1
SWITCH1={RATIONAL R_0=0.4 MM=12 NN=4}
NLIST
NL_CUTOFF=1.2
NL_STRIDE=10
NL_SKIN=0.1
... PIV

PRINT ARG=c1 FILE=colvar.dat FMT=%15.6f

Oxigen atoms (ATOMTYPES=O) are used for the PIV construction, and neighbor lists (NLIST) are used for the calculation of atom-atom distances. Distances are then mapped into numbers from 0 to 1 usign a switching function (SWITCH1={RATIONAL R_0=0.4 MM=12 NN=4}) with a precision of $10^{-3}$ (PRECISION=1000). A complete description of all the keywords can be found here.

When including the example above into a file (e.g. plumed.dat) and running

plumed driver --mf_pdb Ih.pdb --plumed plumed.dat

one gets the PIV distance between the configurations specified in the Ih.pdb and Liq.pdb files. Please note that the order of atoms in Ih.pdb and Liq.pdb files must be the same.

Check that if one computes the distance between two identical configurations the result is zero.