# How-to guides

Task-oriented recipes. Each page solves one concrete problem; pick the one matching your situation. Molecule-level recipes (reading, selection, wrapping, projections, ...) live in [moleculekit's how-to guides](https://software.acellera.com/moleculekit/howto/index.html) - the pages here cover the HTMD layer above that (system building, simulation orchestration, MSM analysis).

## System building

```{toctree}
:maxdepth: 1

system-build-custom-forcefield
system-build-amber-openff
system-build-custombond
```

## Membranes

```{toctree}
:maxdepth: 1

membrane-asymmetric-bilayer
membrane-embed-preequilibrated
```

## Adaptive sampling

```{toctree}
:maxdepth: 1

adaptive-configure
adaptive-goal-function
adaptive-inspect-run
```

## MSM analysis

```{toctree}
:maxdepth: 1

msm-simlist-custom-layout
msm-filter-trajectories
msm-drop-bad-trajectories
msm-bootstrap-errors
msm-interpret-its-plot
msm-plot-fes
msm-extract-state-structures
```

## Force-field and docking tools

```{toctree}
:maxdepth: 1

ffevaluate-energies
docking-poses
```