PLUMED: PLUMED is starting
PLUMED: Version: 2.11.0-dev (git: a740f19-dirty) compiled on Aug 23 2026 at 15:27:33
PLUMED: Please cite these papers when using PLUMED [1][2]
PLUMED: For further information see the PLUMED web page at http://www.plumed.org
PLUMED: Root: /home/runner/opt/lib/plumed
PLUMED: LibraryPath: /home/runner/opt/lib/libplumedKernel.so
PLUMED: For installed feature, see /home/runner/opt/lib/plumed/src/config/config.txt
PLUMED: Molecular dynamics engine: driver
PLUMED: Precision of reals: 8
PLUMED: Running over 1 node
PLUMED: Number of threads: 2
PLUMED: Cache line size: 512
PLUMED: Number of atoms: 100000
PLUMED: File suffix: 
PLUMED: Timestep: 1.000000
PLUMED: KbT: 2.490000
PLUMED: Relevant bibliography:
PLUMED:   [1] The PLUMED consortium, Nat. Methods 16, 670 (2019)
PLUMED:   [2] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)
PLUMED: Please read and cite where appropriate!
PLUMED: Finished setup
PLUMED: Action UNITS
PLUMED:   with label @0
PLUMED:   length: A = 0.1 nm
PLUMED:   energy: kj/mol
PLUMED:   time: ps
PLUMED:   charge: e
PLUMED:   mass: amu
PLUMED:   using physical units
PLUMED:   inside PLUMED, Boltzmann constant is 0.00831446
PLUMED: Action GROUP
PLUMED:   with label WaterO
PLUMED:   list of atoms:
PLUMED:  1 4
PLUMED: Action GROUP
PLUMED:   with label WaterH
PLUMED:   list of atoms:
PLUMED:  2 3 5 6
PLUMED: Action GROUP
PLUMED:   with label GlyN
PLUMED:   list of atoms:
PLUMED:  7
PLUMED: Action GROUP
PLUMED:   with label GlyH
PLUMED:   list of atoms:
PLUMED:  8 9 10
PLUMED: Action GROUP
PLUMED:   with label GlyO1
PLUMED:   list of atoms:
PLUMED:  15
PLUMED: Action GROUP
PLUMED:   with label GlyO2
PLUMED:   list of atoms:
PLUMED:  16
PLUMED: Action GROUP
PLUMED:   with label AllH
PLUMED:   list of atoms:
PLUMED:  2 3 5 6 8 9 10
PLUMED: Action GROUP
PLUMED:   with label Centers
PLUMED:   list of atoms:
PLUMED:  1 4 7 15 16
PLUMED: Action VORONOI_COORDINATION
PLUMED:   with label sp
PLUMED:   VORONOI_COORDINATION assigns 7 atoms over 5 centers with kappa 5
PLUMED:   reducing 5 selected centers with POWER=1 SIGN=ALL
PLUMED: Action VORONOI_DISTANCE
PLUMED:   with label sd_water
PLUMED:   VORONOI_DISTANCE assigns 7 atoms over 5 centers with kappa 5
PLUMED:   reducing 6 explicit center pairs
PLUMED: Action VORONOI_DISTANCE
PLUMED:   with label sd_internal
PLUMED:   VORONOI_DISTANCE assigns 7 atoms over 5 centers with kappa 5
PLUMED:   reducing 2 explicit center pairs
PLUMED: Action COMBINE
PLUMED:   with label sd
PLUMED:   with arguments : 
PLUMED:    scalar with label sd_water 
PLUMED:    scalar with label sd_internal 
PLUMED:   with coefficients: 1.000000 1.000000
PLUMED:   with parameters: 0.000000 0.000000
PLUMED:   and powers: 1.000000 1.000000
PLUMED: Action PRINT
PLUMED:   with label @14
PLUMED:   with stride 1
PLUMED:   with arguments : 
PLUMED:    scalar with label sp 
PLUMED:    scalar with label sd_water 
PLUMED:    scalar with label sd_internal 
PLUMED:    scalar with label sd 
PLUMED:   on file COLVAR
PLUMED:   with format  %f
PLUMED:                                               Cycles        Total      Average      Minimum      Maximum
PLUMED:                                                    1     0.011084     0.011084     0.011084     0.011084
