The prefered method of starting a KIMMDY run is via the command line, though Python entry points are supported as well.
KIMMDY
!kimmdy --help
usage: kimmdy [-h] [--input INPUT] [--loglevel LOGLEVEL] [--logfile LOGFILE]
[--show-plugins] [--generate-jobscript] [--version] [--debug]
[--callgraph]
Welcome to KIMMDY. `kimmdy` runs KIMMDY, further tools are available as
`kimmdy-...` commands. These are `-analysis`, `-modify-top` and `-build-
examples`. Access their help with `kimmdy-... -h.`
options:
-h, --help show this help message and exit
--input INPUT, -i INPUT
Kimmdy input file. Default `kimmdy.yml`
--loglevel LOGLEVEL, -l LOGLEVEL
logging level (CRITICAL, ERROR, WARNING, INFO, DEBUG)
--logfile LOGFILE, -f LOGFILE
logfile
--show-plugins List available plugins
--generate-jobscript Instead of running KIMMDY directly, generate at
jobscript.sh for slurm HPC clusters.You can then run
this jobscript with sbatch jobscript.sh
--version show program's version number and exit
--debug on error, drop into debugger
--callgraph Generate visualization of function calls. Mostly
useful for debugging and documentation.
!kimmdy-analysis --help
usage: kimmdy-analysis [-h] module ...
Welcome to the KIMMDY analysis module. Use this module to analyse existing
KIMMDY runs.
positional arguments:
module
trjcat Concatenate trajectories of a KIMMDY run
energy Plot GROMACS energy for a KIMMDY run
radical_population Plot population of radicals for one or multiple KIMMDY
run(s)
radical_migration Create a json of radical migration events for further
analysis.
rates Plot rates of all possible reactions after a MD run.
Rates must have been saved!
runtime Plot runtime of the tasks of a kimmdy run.
reaction_participation
Plot counts of reaction participation per atom id
options:
-h, --help show this help message and exit
Create plumed input
This module creates input files for plumed based on a topology and index file.
!kimmdy-create-plumed --help
usage: kimmdy-create-plumed [-h] [--entries-to-remove [ENTRIES_TO_REMOVE ...]]
[--stride STRIDE] -p TOP -i INDEX --indexgroup
INDEXGROUP
Build plumed input file. Requires a topology file and a gromacs index file.
options:
-h, --help show this help message and exit
--entries-to-remove [ENTRIES_TO_REMOVE ...]
Either atomnames or bonds, i.e. atomnames separated by
a hyphen that should not be written to the plumed
configuration file. Default: C-N H* O*
--stride STRIDE Frequency of plumed output as multiple of the md
timestep. Default: 100
-p TOP, --top TOP Gromacs topology file path.
-i INDEX, --index INDEX
Gromacs index file path.
--indexgroup INDEXGROUP
Index group name out of which bonds will be written to
the plumed configuration file.
Remove Hydrogen
This module builds or restores the example directory in the package.
!kimmdy-modify-top --help
usage: kimmdy-modify-top [-h] [-p] [--grappa_tag GRAPPA_TAG]
[--grappa_charge_model GRAPPA_CHARGE_MODEL]
[-r REMOVEH [REMOVEH ...]] [-c GRO] [-a]
[-t RESIDUETYPES] [-x RADICALS [RADICALS ...]]
[-w INCLUDE] [-b EXCLUDE]
top out
Welcome to the KIMMDY modify top module
positional arguments:
top GROMACS top file
out Output top file name. Stem reused for gro if
applicabel.
options:
-h, --help show this help message and exit
-p, --parameterize Parameterize topology with grappa. (default: False)
--grappa_tag GRAPPA_TAG
Set grappa model tag for parameterization. (default:
latest)
--grappa_charge_model GRAPPA_CHARGE_MODEL
Set grappa charge model for parameterization.
(default: amber99)
-r REMOVEH [REMOVEH ...], --removeH REMOVEH [REMOVEH ...]
Remove one or more hydrogens by atom nrs in the top
file. (default: None)
-c GRO, --gro GRO If necessary, also apply actions on gro file to create
a compatible gro/top file pair. Output analog to top.
(default: None)
-a, --search_amber_rad
Automatic radical search only implemented for amber.
If you douse another ff, set this to false, and
provide a list of radicalsmanually, if necessary.
(default: False)
-t RESIDUETYPES, --residuetypes RESIDUETYPES
GROMACS style residuetypes file. Necessary for
parameterization with non-amber atom types. (default:
None)
-x RADICALS [RADICALS ...], --radicals RADICALS [RADICALS ...]
Radicals in the system PRIOR to removing hydrogens
with the removeH option. (default: None)
-w INCLUDE, --include INCLUDE
Include certain GROMACS topology molecules in
`Reactive` molecule. Reads molecule names from a csv
file. (default: None)
-b EXCLUDE, --exclude EXCLUDE
Exclude certain GROMACS topology molecules in
`Reactive` molecule. Reads molecule names from a csv
file. (default: None)
Examples
This module builds or restores the example directory in the package.
!kimmdy-build-examples --help
usage: kimmdy-build-examples [-h] [-r [RESTORE]]
Build examples for KIMMDY.
options:
-h, --help show this help message and exit
-r [RESTORE], --restore [RESTORE]
Overwrite input files in existing example directories,
use keyword 'hard' to also delete output files.