utils
utils
Utilities for building plugins, shell convenience functions and GROMACS related functions
Attributes
| Name | Description |
|---|---|
| TopologyAtomAddress | Address to an atom in the topology. |
Functions
| Name | Description |
|---|---|
| check_gmx_version | Check for an existing gromacs installation. |
| get_atominfo_from_atomnrs | Use topology atoms section to convert from atomnr to atomtype |
| get_atomnrs_from_plumedid | Convert from plumedid to atomnr, information from the plumed file is used. |
| get_bondprm_from_atomtypes | Returns bond parameters (b0, kb) for a set of two atomtypes. |
| get_edissoc_from_atomnames | Returns dissociation energy E_dissoc for a set of two atomnames. |
| get_gmx_dir | Returns the path to the gromacs installation |
| get_shell_stdout | Run command in shell and capture stdout. |
| get_task_directories | create list of subdirectories that match the tasks. |
| morse_transition_rate | Calculates reaction rate constant for a bond breaking event. |
| run_gmx | Run GROMACS command in shell. |
| run_shell_cmd | Run command in shell. |
| truncate_sim_files | Truncates latest trr, xtc, edr, and gro to the time to a previous |
check_gmx_version
utils.check_gmx_version(config)
Check for an existing gromacs installation.
If PLUMED is meant to be used it additionally checks for the keyword ‘MODIFIED’ or ‘plumed’ in the version name.
get_atominfo_from_atomnrs
utils.get_atominfo_from_atomnrs(atomnrs, top)
Use topology atoms section to convert from atomnr to atomtype
get_atomnrs_from_plumedid
utils.get_atomnrs_from_plumedid(plumedid, plumed)
Convert from plumedid to atomnr, information from the plumed file is used.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
plumedid |
str | Identifier from a plumed input file (e.g d0). | required |
plumed |
Plumed_dict | Parsed plumed input file | required |
get_bondprm_from_atomtypes
utils.get_bondprm_from_atomtypes(atomtypes, ffbonded)
Returns bond parameters (b0, kb) for a set of two atomtypes.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
atomtypes |
list[str] | Two atomtypes as defined in the respective force field | required |
ffbonded |
dict | Force field ffbonded.itp file parsed through the rtp parser | required |
get_edissoc_from_atomnames
utils.get_edissoc_from_atomnames(atomnames, edissoc, residue='_')
Returns dissociation energy E_dissoc for a set of two atomnames.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
atomnames |
list[str] | Two atomnames as defined in the respective force field | required |
edissoc |
dict | Parsed file with dissociation energies per bond between two atomtypes or elements | required |
residue |
str | Residue for which the atomnames are defined | '_' |
get_gmx_dir
utils.get_gmx_dir(gromacs_alias='gmx')
Returns the path to the gromacs installation
get_shell_stdout
utils.get_shell_stdout(s)
Run command in shell and capture stdout.
get_task_directories
utils.get_task_directories(dir, tasks='all')
create list of subdirectories that match the tasks. If tasks is “all”, all subdirectories are returned.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
dir |
Path | Directory to search for subdirectories | required |
tasks |
Union[list[str], str] | List of steps e.g. [“equilibrium”, “production”]. Or a string “all” to return all subdirectories | 'all' |
morse_transition_rate
utils.morse_transition_rate(r_curr, r_0, dissociation_energy, k_f, frequency_factor=0.288, temperature=300)
Calculates reaction rate constant for a bond breaking event.
Uses the Morse potential model for this calculation. For an array of bond distances of the same bond, first calculates the forces on the bond, then the minima and maxima of the shifted Morse potential to get an energy barrier and finally a reaction rate constant using the Arrhenius equation. For intramolecular reactions, the reaction rate constant is equal to the reaction rate.
The calculation should be according to the derivation in the original KIMMDY paper: DOI: 10.1021/acs.jctc.9b00786
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
r_curr |
list[float] | Bond distances for a single bond, typically from a time series. | required |
r_0 |
float | Equilibrium bond length of the bond. | required |
dissociation |
Dissociation energy of the bond. | required | |
k_f |
float | Spring constant of the bond. | required |
frequency_factor |
float | Prefactor of the Arrhenius equation in [1/ps]. Default value from fitting averaged C_a - N data to gromacs data, see original KIMMDY paper Alternatively 1/2pi sqrt(k/m). | 0.288 |
temperature |
float | Temperature for the Arrhenius equation in GROMACS units. | 300 |
run_gmx
utils.run_gmx(s, cwd=None)
Run GROMACS command in shell.
Adds a ‘-quiet’ flag to the command and checks the return code.
run_shell_cmd
utils.run_shell_cmd(s, cwd=None)
Run command in shell.
truncate_sim_files
utils.truncate_sim_files(files, time, keep_tail=True)
Truncates latest trr, xtc, edr, and gro to the time to a previous point in time.
The files stay in place, the truncated tail is by default kept and renamed to ‘[…xtc].tail’
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
time |
Optional[float] | Time in ps up to which the data should be truncated. | required |
files |
TaskFiles | TaskFiles to get the latest files. | required |