CP2K + PLUMED Dashboard

Project

malonaldehyde_plumed

MD Progress

GPU Utilisation

Current Step

ETA unavailable

Run configuration

Paths and execution settings used by the backend.

Project name

Workflow

Working directory

CP2K binary

Input filename

Output filename

MPI ranks

OpenMP threads

Expected MD steps

Timestep (fs)

Connection mode

Server mode

Launch command

Generated automatically from the run configuration.

A browser cannot execute CP2K directly. Server mode requires a backend service running on the CP2K workstation.

Compound structure input

Upload a molecular structure, paste coordinates, enter SMILES, or use a Ketcher editor.

Input method

Structure file

Supported inputs: XYZ, PDB, MOL, SDF, CIF and CP2K coordinate text.

Coordinate filename

Structure format

Total charge

Multiplicity

Structure summary

Review the structure before starting the calculation.

Atoms

Format

XYZ

Charge

-1

Source

None

Structure content

No molecular structure loaded.

CP2K input

Edit, upload or download the CP2K input file.

&GLOBAL
  PROJECT malonaldehyde_plumed
  RUN_TYPE MD
  PRINT_LEVEL MEDIUM
&END GLOBAL

&FORCE_EVAL
  METHOD Quickstep

&DFT
    BASIS_SET_FILE_NAME BASIS_MOLOPT
    POTENTIAL_FILE_NAME GTH_POTENTIALS
    CHARGE 0

&QS
      METHOD GPW
    &END QS

&MGRID
      CUTOFF 400
      REL_CUTOFF 50
      NGRIDS 5
    &END MGRID

&SCF
      MAX_SCF 100
      EPS_SCF 1.0E-5
      SCF_GUESS ATOMIC

&OT
        PRECONDITIONER FULL_SINGLE_INVERSE
        MINIMIZER DIIS
        ENERGY_GAP 0.001
      &END OT

&OUTER_SCF
        MAX_SCF 10
        EPS_SCF 1.0E-5
      &END OUTER_SCF
    &END SCF

&XC
      &XC_FUNCTIONAL PBE
      &END XC_FUNCTIONAL
    &END XC

&POISSON
      PERIODIC NONE
      PSOLVER MT
    &END POISSON
  &END DFT

&SUBSYS
    &CELL
      ABC 20.0 20.0 20.0
      PERIODIC NONE
    &END CELL

&TOPOLOGY
      COORD_FILE_NAME malonaldehyde_structure.xyz
      COORD_FILE_FORMAT XYZ
    &END TOPOLOGY

&KIND H
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q1
    &END KIND

&KIND C
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q4
    &END KIND

&KIND O
      BASIS_SET DZVP-MOLOPT-GTH
      POTENTIAL GTH-PBE-q6
    &END KIND
  &END SUBSYS
&END FORCE_EVAL

&MOTION
  &MD
    ENSEMBLE NVT
    STEPS 1000
    TIMESTEP 0.5
    TEMPERATURE 300.0

&THERMOSTAT
      TYPE CSVR
      REGION GLOBAL

&CSVR
        TIMECON 20.0
      &END CSVR
    &END THERMOSTAT
  &END MD

&FREE_ENERGY
    METHOD METADYN

&METADYN
      USE_PLUMED .TRUE.
      PLUMED_INPUT_FILE plumed.dat
    &END METADYN
  &END FREE_ENERGY

&PRINT
    &TRAJECTORY
      FORMAT XYZ

&EACH
        MD 10
      &END EACH
    &END TRAJECTORY

&RESTART
      BACKUP_COPIES 3

&EACH
        MD 100
      &END EACH
    &END RESTART
  &END PRINT
&END MOTION

PLUMED input

Generated automatically from the detected donor–H–acceptor pathway; manual editing remains available.

Automatic proton-transfer setup

Detect X–H···X atom IDs, generate PLUMED, validate it and run a one-step preflight.

Automatically detect and generate PLUMED

Run one-step preflight before the main calculation

Detected pathway

SIGMA (Å)

HEIGHT (kJ/mol)

PACE (steps)

BIASFACTOR

Temperature (K)

COLVAR stride

No pathway has been analysed yet.

Automatic parameters are conservative starting values. Validate the final free-energy result scientifically.

Preflight

Not started

Transfer

Not detected

HILLS

Latest SCF

—

Live CP2K output

The server backend can stream or poll the CP2K output file.

Dashboard ready.
Waiting for CP2K job.

COLVAR plot

Selected CV traces from the current or completed run.

COLVAR values

Run files

Input, structure, trajectory, restart, HILLS and output files.