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] [--checkpoint CHECKPOINT]
[--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`
--checkpoint CHECKPOINT, -c CHECKPOINT
File path of a kimmdy.cpt file to restart KIMMDY from
a checkpoint. If a directory is given, the file
kimmdy.cpt in that directory is used.
--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.
Analysis
!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)
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.
options:
-h, --help show this help message and exit
Remove Hydrogen
This module builds or restores the example directory in the package.
!kimmdy-modify-top --help
usage: kimmdy-modify-top [-h] [-p] [-r REMOVEH [REMOVEH ...]] [-c GROFILE]
[-t RESIDUETYPES] [-x RADICALS]
top out
Welcome to the KIMMDY modify top module
positional arguments:
top GROMACS top file
out Output top file name
options:
-h, --help show this help message and exit
-p, --parameterize Parameterize topology with grappa. (default: False)
-r REMOVEH [REMOVEH ...], --removeH REMOVEH [REMOVEH ...]
Remove one or more hydrogens by atom nrs in the top
file. (default: None)
-c GROFILE, --grofile GROFILE
If necessary, also apply actions on gro file to create
a compatible gro/top file pair. (default: None)
-t RESIDUETYPES, --residuetypes RESIDUETYPES
GROMACS style residuetypes file. Necessary for
parameterization with non-amber atom types. (default:
None)
-x RADICALS, --radicals RADICALS
Radicals in the system PRIOR to removing hydrogens
with the removeH option. (default: )
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.