mdpeditor 1.2.5
Edit simulation parameter input files for GROMACS
Requires Python: >=3.8
Keywords: molecular dynamics,GROMACS

# MDP Editor

Easily produce molecular dynamics simulation parameter input for
[GROMACS](https://gitlab.com/gromacs/gromacs).

- say it with words
  - compile pre-defined `.mdp` input parameter blocks reflecting best practices
  for different simulation scenarios
- script parameter file generation and alteration
  - swap parameter blocks when, e.g., simulating with a different force-field
- document the intent of your parameter settings
  - written `.mdp` files store the command that was used to generate them,
  simplifying documentation of simulation run input
- simple input files
  - write only the parameters that you need

## Features

- [x] stable command line interface
- [x] parameter blocks for the most common simulation scenarios
- [x] documentation of pre-defined parameter blocks on the command line
- [x] manually setting specific parameters
- [ ] providing and updating own `.mdp` files -> removed, because this goes against the philosophy of mdpeditor to ensure reproducible research
- [x] option to write minimal output
- [ ] addition of more complex parameter blocks
  - [x] density guided simulations
  - [ ] free energy calculation scenarios
  - [ ] QM/MM
- [ ] parameter evaluation
  - [x] for density guided simulations (calculate spreading width from pixel size)
  - [ ] `nsteps` from setting `simulation-time-in-ns`
- [x] textual user interface
- [ ] graphical user interface
- [x] help text for parameters
- [ ] `grompp` parameter check

## Examples

Prepare an NPT md-simulation with the charmm force-field with sparse output

```bash
mdpeditor type.molecular-dynamics output.minimal force_field.charmm pressure.atmospheric temperature.300K-protein-separate
```

yields

```bash
integrator         = md
dt                 = 0.002
nsteps             = -1
nstxout            = 0
nstvout            = 0
nstfout            = 0
nstlog             = 50000
nstenergy          = 25000
nstxout-compressed = 25000
compressed-x-grps  = Protein
coulombtype        = PME
rcoulomb           = 1.2
vdw-modifier       = Force-switch
rvdw               = 1.2
dispcorr           = no
fourierspacing     = 0.15
tcoupl             = V-rescale
tc-grps            = Protein Non-Protein
tau-t              = 0.1     0.1
ref-t              = 300     300
pcoupl             = C-rescale
pcoupltype         = isotropic
tau-p              = 5.0
compressibility    = 4.5e-5
ref-p              = 1.0
refcoord-scaling   = com
gen-temp           = 300
constraints        = h-bonds
```

---

Show the available pre-defined parameter blocks

```bash
mdpeditor help
```

---

Learn more about parameters for density guided simulations

```bash
mdpeditor --explain density_guided.vanilla
```

---

Describe the `integrator` .mdp option

```bash
mdpeditor --explain integrator
```

## Contributing

You can contribute by [opening a new issue](https://gitlab.com/cblau/mdpeditor/-/issues/new).

### Contributing or changing parameter blocks

Adding a new `.mdp` file in a subdirectory of `mdpeditor/mdpblocks` will add a
new block that is automatically discovered by the python package. The block of
commented first lines (using `;`) will be printed as description of the block.

## Installing and running

Install the latest release from the python package manager

```bash
pip3 install mdpeditor
```

Then run it

```bash
mdpeditor
```

## Installing and running from source (if you must)

Running directly from the shell

```bash
./mdp-editor.py
```

### Build from source (if you must)

We use `setuptools` with a `setup.cfg` and `pyproject.toml` file.

To build a distribution from the source directory install

```bash
pip3 install build
```

Then run this in the source directory to build the distribution on your system

```bash
python3 -m build
```

Eventually, find the build in `dist/` and install the `.tar.gz` file found
there with

```bash
pip install dist/mdpeditor*.tar.gz
```

Make sure to install the right `.tar.gz` if you ran the build command
multiple times.

### Generating a single executable

To generate a single executable that you can run almost anywhere run

```bash
pip3 install pyinstaller
pyinstaller --onefile mdpeditor.spec
```

You will find the executable in

```bash
dist/
```

## Author

Christian Blau