mdpeditor 1.2.5

Description:

mdpeditor 1.2.5

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

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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