KIMMDY config file
KIMMDY config file, see: graeter-group.github.io/kimmdy
| Type | object |
|---|---|
| File match |
kimmdy.yml
kimmdy.yaml
|
| Schema URL | https://catalog.lintel.tools/schemas/schemastore/kimmdy-config-file/latest.json |
| Source | https://raw.githubusercontent.com/graeter-group/kimmdy/main/src/kimmdy/kimmdy-yaml-schema.json |
Validate with Lintel
npx @lintel/lintel checkProperties
Settings for applying a reaction recipe
2 nested properties
Settings related to coordinate/geometry changes when applying a recipe
3 nested properties
MD step from the 'mds' section that is used for relaxation MDs
This is deprecated. Specify in config.changer.coordinates.slow_growth instead.
Whether the chosen MD step is a slow growth/free-energy simulation to relax after applying a reaction recipe. true and yes are equivalent to full for backwards compatibility. morse_only disables using pairs to transition non-bonded interactions as well and only uses morse bonds to emulate simple non-bonded interactions. The empty string means no slow growth.
Settings for parameter changes in the topology file
3 nested properties
Whether to remove bonds from the plumed.dat input file when applying a reaction recipe that breaks a bond. Unless needed for performance optimization, this can be left at false, because the homolysis plugin in kimmdy-reactions also cheeckts to not break non-existing bonds by default (which can be turned off).
Parameterization scheme that is used on the topology file after changes to it
Keyword argument container for the selected parameterization scheme
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>
SLURM HPC options
7 nested properties
Number of nodes
n tasks per node
mincpus
cpus per task
n gpus
Command to (re)submit the jobscript. Default is sbatch. For local testing replace with an empty string do run the jobscript directly.
HPC partition
Don't run the actual simulations, just print the tasks
Don't execute the recipes returned by the chosen reaction, just get the rates (and choose one). KIMMDY will exit after reactions have been queried for the first time in the sequence.
parameterize the topology during the setup task
Working directory. Default is current working directory
Used for output folder if out is not specified
Output folder
Settings for logging
2 nested properties
Logfile name (will result in a path relative to out)
Loglevel
Maximum number of tasks to run. This is useful when a task in the sequence can dymanically add more tasks. 0 means no limit.
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.
KMC algorithm overwrite. Should be set by the reactions, but can be changed here. Not all reactions may support all algorithms.
Number of reactions to be executed in one step by a multi variant of a KMC algorithm.
Scaling parameter for tau in the extrande kmc algorithm.
Topology file
Settings for handling the topology file.
1 nested properties
Specify what moleculetypes will be part of the Reactive moleculetype. By default, solvent and ions are excluded.
3 nested properties
Explicitly include a moleculetype or list of moleculetypes as a space-separated string.
Explicitly exclude a moleculetype or a list as a space-separated string. For example the lipid moleculetype in a bilayer simulation e.g. DPPC POPC'
Explictly set the nrexcl value for the Reactive moleculetype. By default the value is taken from the first found reactive moleculetype.
Coordinate file
Gromaxs index file
File with additional dissociation energy terms. This is used for the homolysis and hydrolysis reactions.
Prefix command for grompp execution on non MPI compiled clusters, e.g., 'srun --ntasks=1'.
Gromacs alias. e.g. gmx or mpirun gmx_mpi
Prefix command for mdrun execution on non MPI compiled clusters, e.g., 'srun --ntasks=1'.
Flags passed to gmx mdrun. Default -maxh 24 -dlb yes
Force field directory (looks for .ff in cwd if not set)
GROMACS rtp file that contains residuetypes. Looks for aminoacids.rtp it not set. KIMMDY will first look in the current working directory and then relative to the forecfield directory.
space-separated string of radical atom ids, can be empty
.dat file containing plumed config
.tpr file of a finished simulation for starting directly with a reaction
.trr file of a finished simulation for starting directly with a reaction
.xtc file of a finished simulation for starting directly with a reaction
.mdp file of a finished simulation for starting directly with a reaction
This is deprecated and no longer required.
Restart or continue from a previous run (in config.out) instead of starting from scratch
Settings for MD steps, e.g. mdp files, plumed files, etc.
Settings for reactions
6 nested properties
Save recipes as csv during the reactions step