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README.md

Template for MoSDeF- and GROMACS-centric project managed with signac

See generic signac template and a fork

Installation

Install these packages:

Install other dependencies:

python setup.py install

Get started:

Initialize project:

python src/init.py

Build systems and perform energy minimization:

python src/project.py run initialize
python src/project.py run em  # energy minimization

Submit equilibration and production runs to the cluster (can also be run locally as above)

python src/project.py submit -o equil
python src/project.py submit -o sample

At any time you can evaluate the status of each job with:

python src/project.py status -d

Analyze system (here, simple timeseries plots of density)

python analysis/calc_density.py

Look at the PDF file located in the workspace directory. It should look something like this:

image

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