Command line tool¶
The metaFALCON command line tool allows to perform molecular dynamics, metadynamics and multistate metadynamics simulations and provides several analysis utilities.
usage: metaFALCON [-h]
{gui,initial,run,analyze,log2xyz,reconstruct,reset,custom,version}
...
Sub-commands:¶
gui¶
GUI Application aimed for the input preparation of molecular dynamics, metadynamics or multistate metadynamics simulations with the metaFALCON package.
metaFALCON gui [-h]
initial¶
Generate initial conditions randomly or take coordinates and velocities from previous calculation.
metaFALCON initial [-h] [--fromlog] [--step STEP] [--source SOURCE] [--random]
[--temp TEMP] [--xyz XYZ]
Named Arguments¶
| --fromlog | use coordinates and velocities from log-file of previous calculation Default: False |
| --step | step number (-1 = last step) Default: -1 |
| --source | directory that contains the log-file Default: “.” |
| --random | generate random velocities Default: False |
| --temp | temperature (K) for the generation of random velocitites Default: 300 |
| --xyz | file that contains the coordinates used for random velocities generation Default: “initial.xyz” |
run¶
Run the dynamics simulation according to the input parameters given in meta-config.json.
metaFALCON run [-h]
analyze¶
Analyze trajectory geometries and energies / temperature (from dynamics-*.log). Option defaults are taken from the meta-config.json file.
metaFALCON analyze [-h] [--stride STRIDE] [--start START] [--end END]
[--nlog NLOG] [--reset]
Named Arguments¶
| --stride | number of trajectory frames per step Default: 1 |
| --start | first trajectory frame to be parsed Default: 0 |
| --end | last trajectory frame to be parsed (-1 means last) Default: -1 |
| --nlog | index of log-file to be parsed (-1 means all log-files) Default: -1 |
| --reset | reset stride, start, end and nlog values to default and do not take them from the meta-config.json file Default: False |
log2xyz¶
Convert geometries in dynamics-*.log to xyz-format saved in dynamics.xyz. Option defaults are taken from the meta-config.json file.
metaFALCON log2xyz [-h] [--stride STRIDE] [--start START] [--end END]
[--nlog NLOG] [--single] [--reset]
Named Arguments¶
| --stride | number of trajectory frames per step Default: 1 |
| --start | first trajectory frame to be parsed Default: 0 |
| --end | last trajectory frame to be parsed (-1 means last) Default: -1 |
| --nlog | index of log-file to be parsed (-1 means all log-files) Default: -1 |
| --single | create single dynamics-i.xyz for every log-file Default: False |
| --reset | reset stride, start, end and nlog values to default and do not take them from the meta-config.json file Default: False |
reconstruct¶
Reconstruct the metadynamics potential using data in vg_centers.dat and parameters in meta-config.json.
metaFALCON reconstruct [-h] [--ngauss NGAUSS] [--animate] [--stride STRIDE]
[--extension EXTENSION] [--unit UNIT] [--vg VG]
Named Arguments¶
| --ngauss | use only the first ngauss gaussians (Default: all) |
| --animate | animate the potential evolution Default: False |
| --stride | number of gaussians per animation frame Default: 1 |
| --extension | metadynamics identifier used in the config file (Default: None) |
| --unit | unit of the plotted metadynamics potential (eV | kcalpermol | Ha) Default: “eV” |
| --vg | plot the metadynamics potential instead of the free energy surface (eV | kcalpermol | Ha) Default: False |
reset¶
Reset metadynamics folder to specific time step.
metaFALCON reset [-h] [--step STEP]
Named Arguments¶
| --step | step from which the dynamics should be restarted Default: 0 |
custom¶
Copy a template file cvcustom.py into the current working directory that can be used for the setup of user-defined collective variables.
metaFALCON custom [-h]