Edit simulation parameter input files for GROMACS
Project description
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
- compile pre-defined
- 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
- written
- 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 - option to write minimal output
- addition of more complex parameter blocks
- density guided simulations
- free energy calculation scenarios
- QM/MM
- parameter evaluation (like
nsteps
from settingsimulation-time-in-ns
) - textual user interface
- graphical user interface
- help text for parameters
-
grompp
parameter check
Examples
Compile the pre-defined block force_field.charmm
and sets nsteps = 100
in the output
mdpeditor compile force_field.charmm nsteps=100
yields
dt = 0.002
nsteps = 100
coulombtype = PME
rcoulomb = 1.2
vdw-modifier = Force-switch
rvdw = 1.2
dispcorr = no
fourierspacing = 0.15
constraints = h-bonds
Write only values that were set when compiling pressure.atmospheric
with
force_field.charmm
, skip all defaults
mdpeditor compile pressure.atmospheric force_field.charmm
Show the available pre-defined parameter blocks
mdpeditor compile help
Learn more about a certain parameter block
mdpeditor explain density_guided.vanilla
Add atomspheric pressure coupling to a user-defined .mdp file, discarding all
non-GROMACS entries in user.mdp
.
mdpeditor compile user.mdp pressure.atmospheric
Describe the integrator
parameter
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.
Note that once you built an executable as described above, the parameter blocks are packaged with the executable and cannot be changed.
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
Installation with pip
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
Project details
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