KIMMDY Options

Autocompletion

KIMMDY comes with autocompletion for the kimmdy.yml file. You can add the schema to the configuration of the yaml-language-server in your editor (e.g. VS Code via the YAML extension or Neovim via lspconfig). To associate kimmdy.yml files with KIMMDY, add the following to your

VS Code settings

settings.json
"yaml.schemas": {
    "https://raw.githubusercontent.com/hits-mbm-dev/kimmdy/main/src/kimmdy/kimmdy-yaml-schema.json": "kimmdy.yml",
}

Neovim settings

init.lua
require("lspconfig").yamlls.setup({
  on_attach = on_attach,
  capabilities = capabilities,
  flags = lsp_flags,
  settings = {
    yaml = {
      schemas = {
        ["https://raw.githubusercontent.com/hits-mbm-dev/kimmdy/main/src/kimmdy/kimmdy-yaml-schema.json"] = "kimmdy.yml",
      },
    },
  },
})

All Options

The following is a list of the options that can be set in the kimmdy.yml file. It includes reactions currently available in KIMMDY as plugins. Nested options are separated by a .. * denotes an arbitrary name for a section. The key for a section is bold.

Table 1: KIMMDY options
Option Description Type Default
dryrun Don’t run the actual simulations, just print the tasks bool False
write_checkpoint Write checkpoints to continue a KIMMDY run from. Default True bool True
cwd Working directory. Default is current working directory Path
name Used for output folder if out is not specified str kimmdy
out Output folder Path
log Settings for logging
max_tasks Maximum number of tasks to run. This is useful when a task in the sequence can dymanically add more tasks. 0 means no limit. int 0
max_hours Stop KIMMDY after max_hours hours. Set this lower than the limit of your HPC cluster for use with a re-submit jobscript. 0 Means no limit. int 0
kmc KMC algorithm overwrite. Should be set by the reactions, but can be changed here. str
tau_scale Scaling parameter for tau in the extrande kmc algorithm. float 1.0
top Topology file Path topol.top
gro Coordinate file Path conf.gro
ndx Gromaxs index file Path index.ndx
gromacs_alias Gromacs alias. e.g. gmx or mpirun gmx_mpi str gmx
gmx_mdrun_flags Flags passed to gmx mdrun. Default -maxh 24 -dlb yes str -maxh 24 -dlb yes
ff Force field directory (looks for .ff in cwd if not set) Path *.ff
plumed .dat file containing plumed config Path
tpr .tpr file of a finished simulation for starting directly with a reaction Path
trr .trr file of a finished simulation for starting directly with a reaction Path
mds Settings for MD steps, e.g. mdp files, plumed files, etc.
mds.*.mdp MDP file for the MD step Path
mds.*.use_plumed Whether plumed should be used for this run or not bool False
changer Settings for applying a reaction recipe
changer.coordinates.md MD step from the ‘mds’ section that is used for relaxation MDs str
changer.coordinates.slow_growth Whether the chosen MD step is a slow growth/free-energy simulation bool False
changer.topology.parameterization Parameterization scheme that is used on the topology file after changes to it str basic
sequence List of tasks. Each task can be a string (the name of the task) or an object with the task name and a multiplicity mult: <int> Sequence
reactions Settings for reactions
plot_rates Plot the reaction rates during the reactions step bool True
save_recipes Save recipes as csv during the reactions step bool True

Example kimmdy.yml Files

kimmdy.yml
dryrun: false
max_tasks: 100
name: 'hat_tf_000'
gromacs_alias: 'gmx'
top: 'Ala_out.top'
gro: 'npt.gro'
ndx: 'index.ndx'
mds:
  equilibrium:
    mdp: 'md.mdp'
  relax:
    mdp: 'md_slow.mdp'
changer:
  coordinates:
    md: 'relax'      
reactions:
  hat_reaction:
    frequency_factor: 100000000
    h_cutoff: 3
    polling_rate: 1

sequence:
- equilibrium
- mult: 2
  tasks:
  - equilibrium
  - reactions
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