Free energy surface of system [fes]

Estimate the free energy surface from the [histogram] action

This uses the given temperature to calculate the free energy of each histogram bin. The output is aligned to have the minimum at zero.

It can also plot the FES directly via matplotlib.

stride: int

Time steps between FES calculations.

kt: float

Thermal energy of the system, should usually be the same as the one specified in the [ld] section

filename: string, optional

Filename to write the FES to.

write-stride: int, optional

Write FES to file every n time steps (filename will be appended by _t (with the current time step t). If not specified the FES will only be written once at the end of the simulation.

fmt: string, defaults to “%14.9”

c-style format specifier used when writing data to file

plot-filename: string, optional

If specified, the FES will be plotted and saved to the specified path. This works only for 1D and 2D.

plot-stride: int, optional

Plot FES to file every n time steps, not only at the end of the simulation

plot-domain: list of floats, optional

Range of free energy values that should be shown in plot

Example

Calculate FES every 100 steps, save it to file every 500 steps and save a plot at the end of the simulation:

[fes]
stride: 100
write-stride: 500
filename: fes
plot-filename: fes.png
plot-domain: 0, 8.5