Package: mdpeditor
MDP EditorEasily produce molecular dynamics simulation parameter input forGROMACS.say it with wordscompile pre-defined.mdpinput parameter blocks reflecting best practices
for different simulation scenariosscript parameter file generation and alterationswap parameter blocks when, e.g., simulating with a different force-fielddocument the intent of your parameter settingswritten.mdpfiles store the command that was used to generate them,
simplifying documentation of simulation run inputsimple input fileswrite only the parameters that you needFeaturesstable command line interfaceparameter blocks for the most common simulation scenariosdocumentation of pre-defined parameter blocks on the command linemanually setting specific parametersproviding and updating own.mdpfiles -> removed, because this goes against the philosophy of mdpeditor to ensure reproducible researchoption to write minimal outputaddition of more complex parameter blocksdensity guided simulationsfree energy calculation scenariosQM/MMparameter evaluationfor density guided simulations (calculate spreading width from pixel size)nstepsfrom settingsimulation-time-in-nstextual user interfacegraphical user interfacehelp text for parametersgromppparameter checkExamplesPrepare an NPT md-simulation with the charmm force-field with sparse outputmdpeditortype.molecular-dynamicsoutput.minimalforce_field.charmmpressure.atmospherictemperature.300K-protein-separateyieldsintegrator=mddt=0.002nsteps=-1nstxout=0nstvout=0nstfout=0nstlog=50000nstenergy=25000nstxout-compressed=25000compressed-x-grps=Proteincoulombtype=PMErcoulomb=1.2
vdw-modifier=Force-switchrvdw=1.2dispcorr=nofourierspacing=0.15tcoupl=V-rescale
tc-grps=ProteinNon-Protein
tau-t=0.10.1
ref-t=300300pcoupl=C-rescalepcoupltype=isotropic
tau-p=5.0compressibility=4.5e-5
ref-p=1.0
refcoord-scaling=com
gen-temp=300constraints=h-bondsShow the available pre-defined parameter blocksmdpeditorhelpLearn more about parameters for density guided simulationsmdpeditor--explaindensity_guided.vanillaDescribe theintegrator.mdp optionmdpeditor--explainintegratorContributingYou can contribute byopening a new issue.Contributing or changing parameter blocksAdding a new.mdpfile in a subdirectory ofmdpeditor/mdpblockswill 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 runningInstall the latest release from the python package managerpip3installmdpeditorThen run itmdpeditorInstalling and running from source (if you must)Running directly from the shell./mdp-editor.pyBuild from source (if you must)We usesetuptoolswith asetup.cfgandpyproject.tomlfile.To build a distribution from the source directory installpip3installbuildThen run this in the source directory to build the distribution on your systempython3-mbuildEventually, find the build indist/and install the.tar.gzfile found
there withpipinstalldist/mdpeditor*.tar.gzMake sure to install the right.tar.gzif you ran the build command
multiple times.Generating a single executableTo generate a single executable that you can run almost anywhere runpip3installpyinstaller
pyinstaller--onefilemdpeditor.specYou will find the executable indist/AuthorChristian Blau