MDP Editor

Easily produce molecular dynamics simulation parameter input for 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

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

Examples

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

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

yields

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

mdpeditor help

Learn more about parameters for density guided simulations

mdpeditor --explain density_guided.vanilla

Describe the integrator .mdp option

mdpeditor --explain integrator

Contributing

You can contribute by opening a new issue.

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

pip3 install mdpeditor

Then run it

mdpeditor

Installing and running from source (if you must)

Running directly from the shell

./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

pip3 install build

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

python3 -m build

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

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

pip3 install pyinstaller
pyinstaller --onefile mdpeditor.spec

You will find the executable in

dist/

Author

Christian Blau