How to use coordination numbers to run metadynamics based path cv?

[Xiaomei]

Dear all,

I am trying to reproduce the metadynamics simulation based on Path CV from 10.1073/pnas.1512486112. In the PLUMED documentation, the TYPE parameter for PATH is described as: "( default=OPTIMAL-FAST ) the manner in which distances are calculated. More information on the different metrics that are available in PLUMED can be found in the section of the manual on Distances from reference configurations". After reviewing the Distances from reference configurations page, I found that TARGET seems to be able to calculate distances from reference structures using coordination numbers. However, I'm not sure how to combine TARGET with PATH. Does anyone know how to do this? Many thanks.

Below are my reference structure file and coordination number definitions in plumed.dat based on the literature.

plumed.dat:

```bash
UNITS LENGTH=A

h: GROUP ATOMS=1-3
c: GROUP ATOMS=4
n: GROUP ATOMS=5
o: GROUP ATOMS=6

c_n: COORDINATIONNUMBER SPECIESA=c SPECIESB=n SWITCH={RATIONAL D_0=0 R_0=1.8} MEAN
c_o: COORDINATIONNUMBER SPECIESA=c SPECIESB=o SWITCH={RATIONAL D_0=0 R_0=1.8} MEAN
c_h: COORDINATIONNUMBER SPECIESA=c SPECIESB=h SWITCH={RATIONAL D_0=0 R_0=1.5} MEAN
n_c: COORDINATIONNUMBER SPECIESA=n SPECIESB=c SWITCH={RATIONAL D_0=0 R_0=1.8} MEAN
n_o: COORDINATIONNUMBER SPECIESA=n SPECIESB=o SWITCH={RATIONAL D_0=0 R_0=1.8} MEAN
n_h: COORDINATIONNUMBER SPECIESA=n SPECIESB=h SWITCH={RATIONAL D_0=0 R_0=1.5} MEAN
o_n: COORDINATIONNUMBER SPECIESA=o SPECIESB=n SWITCH={RATIONAL D_0=0 R_0=1.8} MEAN
o_c: COORDINATIONNUMBER SPECIESA=o SPECIESB=c SWITCH={RATIONAL D_0=0 R_0=1.8} MEAN
o_h: COORDINATIONNUMBER SPECIESA=o SPECIESB=h SWITCH={RATIONAL D_0=0 R_0=1.5} MEAN
```

reference.pdb:

```bash
ITLE     PDB file created by CP2K version 9.1 (revision git:d8d7100)
AUTHOR    2025-04-14 17:00:21
REMARK    Step 0, time = .000, E = -33.4033961266
CRYST1    9.600    9.600    9.600  90.00  90.00  90.00
ATOM      1 H1                  -5.686 -20.926   9.672  0.00  0.00           H
ATOM      2 H2                  -5.040 -19.628  10.215  0.00  0.00           H
ATOM      3 H3                  -6.510 -19.479   9.483  0.00  0.00           H
ATOM      4 C1                   5.235   1.685   2.900  0.00  0.00           C
ATOM      5 N1                  -5.986 -20.057  10.130  0.00  0.00           N
ATOM      6 O1                   5.791   2.236   2.079  0.00  0.00           O
END
REMARK    Step 0, time = .000, E = -33.4427802517
CRYST1    9.600    9.600    9.600  90.00  90.00  90.00
ATOM      1 H1                  -2.010   3.588   1.502  0.00  0.00           H
ATOM      2 H2                  -2.734   1.836   2.973  0.00  0.00           H
ATOM      3 H3                  -3.692   1.150   1.806  0.00  0.00           H
ATOM      4 C1                  -2.851   3.000   1.213  0.00  0.00           C
ATOM      5 N1                  -3.101   1.914   2.060  0.00  0.00           N
ATOM      6 O1                  -3.544   3.377   0.245  0.00  0.00           O
END
```